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Feliu C, Konecki C, Vautier D, Rogier J, Gozalo C, Cazaubon Y, Djerada Z. Comparison of two acquisition modes in mass spectrometry for quantification of 12 antibiotics, including beta-lactams, linezolid, fluoroquinolones and clindamycin: Multiple reactions monitoring (MRM) and fullMS/dd-MS 2. Anal Biochem 2024; 690:115507. [PMID: 38513768 DOI: 10.1016/j.ab.2024.115507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/18/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
The quantification of antibiotics, using mass spectrometry, for monitoring therapeutic drugs is a key benefit in infection management. After an easy work-up of plasma samples, analysis were performed using both two widely used acquisition modes: MRM for the triple quadrupole spectrometer and fullMS/ddMS2 for the HRMS to quantify twelve antibiotics. Comparison between the two acquisition modes were performed. Validation parameters and sample values were used as comparison criteria. The results indicated a good correlation between the two methods, with an advantage for HRMS concerning the matrix effect. Both methods were applied to routine therapeutic drug monitoring.
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Affiliation(s)
- Catherine Feliu
- Department of Pharmacology, UR 3801, SFR CAP-Santé, Reims University Hospital, 51 rue Cognacq-Jay, CEDEX, 51095, Reims, France.
| | - Celine Konecki
- Department of Pharmacology, UR 3801, SFR CAP-Santé, Reims University Hospital, 51 rue Cognacq-Jay, CEDEX, 51095, Reims, France
| | - Damien Vautier
- Department of Pharmacology, UR 3801, SFR CAP-Santé, Reims University Hospital, 51 rue Cognacq-Jay, CEDEX, 51095, Reims, France
| | - Jessica Rogier
- Department of Pharmacology, UR 3801, SFR CAP-Santé, Reims University Hospital, 51 rue Cognacq-Jay, CEDEX, 51095, Reims, France
| | - Claire Gozalo
- Department of Pharmacology, UR 3801, SFR CAP-Santé, Reims University Hospital, 51 rue Cognacq-Jay, CEDEX, 51095, Reims, France
| | - Yoann Cazaubon
- Institute Desbrest of Epidemiology and Public Health, INSERM, University Montpellier, 34000, Montpellier, France; Department of Pharmacology, Montpellier University Hospital, Avenue du Doyen Gaston Giraud, 34090, Montpellier, France
| | - Zoubir Djerada
- Department of Pharmacology, UR 3801, SFR CAP-Santé, Reims University Hospital, 51 rue Cognacq-Jay, CEDEX, 51095, Reims, France
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Zhang J, Wei L, Miao J, Yu Y, Yu N, Hu Q, Chen H, Chen Y. Authenticity identification of animal species in characteristic milk by integration of shotgun proteomics and scheduled multiple reaction monitoring (MRM) based on tandem mass spectrometry. Food Chem 2024; 436:137736. [PMID: 37863000 DOI: 10.1016/j.foodchem.2023.137736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/19/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
Milk is one of the oldest natural dairies with high value, which has different species including cow, camel, donkey, goat, sheep, buffalo, yak and et al. However, economically motivated adulteration of non-cow milk with cheaper cow milk occurs frequently. To develop a high-throughput approach for milk species authentication, integration of shotgun proteomics and scheduled multiple reaction monitoring (MRM) was developed. In total, 37 specific peptides were screened as unique to different species. Specific peptides processing stability was investigated under different treatment (heat, pressure, fermentation). Subsequently, four quantitative ion pairs of peptides from cow milk and six quantitative ion pairs of peptides from six non-cow milks were selected for the adulteration quantitative analysis. The method is capable of detection adulteration in the range of 1%-100%, and the quantitative recoveries ranged from 91.07% to 111.75%. The results suggested that combination of shotgun proteomics and MRM had potential for the milk species authentication.
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Affiliation(s)
- Jiukai Zhang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Liyang Wei
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Jinliang Miao
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Yue Yu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China; School of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Ning Yu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Qian Hu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - He Chen
- Institute of Quality Standard & Testing Technology for Agro-products, Xinjiang Academy of Agricultural Sciences, 830091, PR China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China.
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Hou J, Deng Q, Qiu X, Liu S, Li Y, Huang C, Wang X, Zhang Q, Deng X, Zhong Z, Zhong W. Proteomic analysis of plasma proteins from patients with cardiac rupture after acute myocardial infarction using TMT-based quantitative proteomics approach. Clin Proteomics 2024; 21:18. [PMID: 38429673 PMCID: PMC10908035 DOI: 10.1186/s12014-024-09474-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 02/23/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Cardiac rupture (CR) is a rare but catastrophic mechanical complication of acute myocardial infarction (AMI) that seriously threatens human health. However, the reliable biomarkers for clinical diagnosis and the underlying signaling pathways insights of CR has yet to be elucidated. METHODS In the present study, a quantitative approach with tandem mass tag (TMT) labeling and liquid chromatography-tandem mass spectrometry was used to characterize the differential protein expression profiles of patients with CR. Plasma samples were collected from patients with CR (n = 37), patients with AMI (n = 47), and healthy controls (n = 47). Candidate proteins were selected for validation by multiple reaction monitoring (MRM) and enzyme-linked immunosorbent assay (ELISA). RESULTS In total, 1208 proteins were quantified and 958 differentially expressed proteins (DEPs) were identified. The difference in the expression levels of the DEPs was more noticeable between the CR and Con groups than between the AMI and Con groups. Bioinformatics analysis showed most of the DEPs to be involved in numerous crucial biological processes and signaling pathways, such as RNA transport, ribosome, proteasome, and protein processing in the endoplasmic reticulum, as well as necroptosis and leukocyte transendothelial migration, which might play essential roles in the complex pathological processes associated with CR. MRM analysis confirmed the accuracy of the proteomic analysis results. Four proteins i.e., C-reactive protein (CRP), heat shock protein beta-1 (HSPB1), vinculin (VINC) and growth/differentiation factor 15 (GDF15), were further validated via ELISA. By receiver operating characteristic (ROC) analysis, combinations of these four proteins distinguished CR patients from AMI patients with a high area under the curve (AUC) value (0.895, 95% CI, 0.802-0.988, p < 0.001). CONCLUSIONS Our study highlights the value of comprehensive proteomic characterization for identifying plasma proteome changes in patients with CR. This pilot study could serve as a valid foundation and initiation point for elucidation of the mechanisms of CR, which might aid in identifying effective diagnostic biomarkers in the future.
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Affiliation(s)
- Jingyuan Hou
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
- GuangDong Engineering Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, Guangdong, 514031, China
| | - Qiaoting Deng
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Xiaohong Qiu
- Meizhou clinical Medical School, Guangdong Medical University, Meizhou, Guangdong, 514031, China
| | - Sudong Liu
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Youqian Li
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Changjing Huang
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Xianfang Wang
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Qunji Zhang
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Xunwei Deng
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Zhixiong Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China.
| | - Wei Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China.
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von Törne WJ, Klyk-Seitz UA, Piechotta C. Developing a GC-EI-MS/MS method for quantifying warfarin and five hydroxylated metabolites generated by the Fenton reaction. Environ Sci Pollut Res Int 2024; 31:16986-16994. [PMID: 38329665 PMCID: PMC10894117 DOI: 10.1007/s11356-024-32133-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Since the 1950s, Warfarin has been used globally as both a prescription drug and a rodenticide. Research has shown that warfarin and other rodenticides are present in the environment and food chain. However, emerging contaminants are subject to degradation by biotic and abiotic processes and advanced oxidation processes. In some cases, detecting the parent compound may not be possible due to the formation of structurally changed species. This approach aims to identify hydroxylated transformation products of warfarin in a laboratory setting, even after the parent compound has undergone degradation. Therefore, the Fenton reaction is utilized to insert hydroxylation into the parent compound, warfarin, by hydroxyl and hydroperoxyl radicals generated by Fe2+/Fe3+ redox reaction with hydrogen peroxide. Using multiple reaction monitoring, a GC-MS/MS method, incorporating isotopically labeled reference compounds, is used to quantify the expected derivatized species. The analytes are derivatized using trimethyl-3-trifluoromethyl phenyl ammonium hydroxide, and the derivatization yield of warfarin is determined by using isotopically labeled reference compounds. The method has a linear working range of 30 to 1800 ng/mL, with detection limits ranging from 18.7 to 67.0 ng/mL. The analytes are enriched using a C18-SPE step, and the recovery for each compound is calculated. The Fenton reaction generates all preselected hydroxylated transformation products of warfarin. The method successfully identifies that 4'-Me-O-WAR forms preferentially under the specified experimental conditions. By further optimizing the SPE clean-up procedures, this GC-MS-based method will be suitable for detecting transformation products in more complex matrices, such as environmental water samples. Overall, this study provides a better understanding of warfarin's degradation and offers a robust analytical tool for investigating its transformation products.
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Affiliation(s)
- Wipert Jannik von Törne
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
- Technischen Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Urszula-Anna Klyk-Seitz
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Christian Piechotta
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.
- Technischen Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
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Pinto N, Nissa MU, Yashwanth BS, Sathiyanarayanan A, Pai MGJ, Srivastava S, Goswami M. Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda. Comp Biochem Physiol Part D Genomics Proteomics 2024; 50:101221. [PMID: 38430708 DOI: 10.1016/j.cbd.2024.101221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
Edwardsiella tarda (Et) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of Labeo rohita (rohu) kidney to Et are poorly understood. A proteomic and histopathological analysis was performed for the rohu kidney after Et infection. The histopathology of the infected rohu kidney showed vacuolation and necrosis. After LC-MS/MS analysis, ~1240 proteins were identified with ≥2 unique peptides. A total of 96 differentially abundant proteins (DAPs) were observed between the control and Et infected group (ET). Metascape and STRING analysis were used for the gene ontology (GO), and protein-protein interaction network (PPI) for the significant pathways of DAPs. In PPI, low-abundant proteins were mapped to metabolic pathways and oxidative phosphorylation (cox5ab, uqcrfs1). High-abundance proteins were mapped to ribosomes (rplp2), protein process in the ER (hspa8), and immune system (ptgdsb.1, muc2). Our label-free proteomic approach in the rohu kidney revealed abundant enriched proteins involved in vesicle coat (ehd4), complement activation (c3a.1, c9, c7a), phagosome (thbs4, mapk1), metabolic reprogramming (hao1, glud1a), wound healing (vim, alox5), and the immune system (psap) after Et infection. A targeted proteomics approach of multiple reaction monitoring (MRM) validated the DAPs (nprl3, ambp, vmo1a, hspg2, muc2, hao1 and glud1a) between control and ET. Overall, the current analysis of histology and proteome in the rohu kidney provides comprehensive data on pathogenicity and the potential immune proteins against Et.
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Affiliation(s)
- Nevil Pinto
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India. https://twitter.com/pintonevil8
| | - Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - B S Yashwanth
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India
| | - A Sathiyanarayanan
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India. https://twitter.com/Sanjeeva_IITB
| | - Mukunda Goswami
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India.
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Shi F, Wang Y, Chang Y, Liu K, Xue C. Establishment of a targeted proteomics method for the quantification of collagen chain: Revealing the chain stoichiometry of heterotypic collagen fibrils in sea cucumber. Food Chem 2024; 433:137335. [PMID: 37678116 DOI: 10.1016/j.foodchem.2023.137335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/27/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Collagen is the most abundant and important structural biomacromolecule in sea cucumbers. The sea cucumber collagen fibrils were previously confirmed to be heterotypic, nevertheless, the stoichiometry of collagen α-chains governing the complexity of collagen fibrils is still poorly understood. Herein, four representative collagen α-chains in sea cucumber including two clade A fibrillar collagens, one clade B fibrillar collagen, and one fibril-associated collagen with interrupted triple helices were selected. After the screening of signature peptides and optimization of multiple reaction monitoring (MRM) acquisition parameters including fragmentation, collision energy, and ion transition, a feasible MRM-based method was established. Consequently, the stoichiometry of the four collagen chains was determined to be approximately 100:54:3:4 based on the method. The assembly forms of sea cucumber collagen fibrils were further hypothesized according to the chain stoichiometry. This study facilitated the quantification of collagen and understanding of the collagen constituents in sea cucumber.
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Affiliation(s)
- Feifei Shi
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yanchao Wang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China.
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China; Qingdao Marine Science and Technology Center, 1 Wenhai Road, Qingdao 266237, China.
| | - Kaimeng Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China; Qingdao Marine Science and Technology Center, 1 Wenhai Road, Qingdao 266237, China
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Luque-Córdoba D, Calderón-Santiago M, Rangel-Zúñiga OA, Camargo A, López-Miranda J, Priego-Capote F. Comprehensive profiling of ceramides in human serum by liquid chromatography coupled to tandem mass spectrometry combining data independent/dependent acquisition modes. Anal Chim Acta 2024; 1287:342115. [PMID: 38182388 DOI: 10.1016/j.aca.2023.342115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/26/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
Ceramides are sphingolipids with a structural function in the cell membrane and are involved in cell differentiation, proliferation and apoptosis. Recently, these chemical species have been pointed out as potential biomarkers in different diseases, due to their abnormal levels in blood. In this research, we present an overall strategy combining data-independent and dependent acquisitions (DIA and DDA, respectively) for identification, confirmation, and quantitative determination of ceramides in human serum. By application of liquid chromatography-tandem mass spectrometry (LC-MS/MS) method in DIA mode we identified 49 ceramides including d18:1, d18:0, d18:2, d16:1, d17:1 and t18:0 species. Complementary, quantitative determination of ceramides was based on a high-throughput and fully automated method consisting of solid-phase extraction on-line coupled to LC-MS/MS in DDA to improve analytical features avoiding the errors associated to sample processing. Quantitation limits were at pg mL-1 level, the intra-day and between-days variability were below 20 and 25 %, respectively; and the accuracy, expressed as bias, was always within ±25 %. The proposed method was tested with the CORDIOPREV cohort in order to obtain a qualitative and quantitative profiling of ceramides in human serum. This characterization allowed identifying d18:1 ceramides as the most concentrated with 70.8% of total concentration followed by d18:2 and d18:0 with 13.0 % and 8.8 %, respectively. Less concentrated ceramides, d16:1, d17:1 and t18:0, reported a 7.1 % of the total content. Combination of DIA and DDA LC-MS/MS analysis enabled to profile qualitative and quantitatively ceramides in human serum.
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Affiliation(s)
- D Luque-Córdoba
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; Chemical Institute for Energy and Environment (IQUEMA), Campus of Rabanales, University of Córdoba, Córdoba, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Consortium for Biomedical Research in Frailty & Healthy Ageing, CIBERFES, Carlos III Institute of Health, Spain
| | - M Calderón-Santiago
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; Chemical Institute for Energy and Environment (IQUEMA), Campus of Rabanales, University of Córdoba, Córdoba, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Consortium for Biomedical Research in Frailty & Healthy Ageing, CIBERFES, Carlos III Institute of Health, Spain
| | - O A Rangel-Zúñiga
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, 14004, Cordoba, Spain; Department of Medical and Surgical Science, University of Cordoba, 14004, Córdoba, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - A Camargo
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, 14004, Cordoba, Spain; Department of Medical and Surgical Science, University of Cordoba, 14004, Córdoba, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - J López-Miranda
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, 14004, Cordoba, Spain; Department of Medical and Surgical Science, University of Cordoba, 14004, Córdoba, Spain; CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - F Priego-Capote
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; Chemical Institute for Energy and Environment (IQUEMA), Campus of Rabanales, University of Córdoba, Córdoba, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Consortium for Biomedical Research in Frailty & Healthy Ageing, CIBERFES, Carlos III Institute of Health, Spain.
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Piarulli F, Banfi C, Ragazzi E, Gianazza E, Munno M, Carollo M, Traldi P, Lapolla A, Sartore G. Multiplexed MRM-based proteomics for identification of circulating proteins as biomarkers of cardiovascular damage progression associated with diabetes mellitus. Cardiovasc Diabetol 2024; 23:36. [PMID: 38245742 PMCID: PMC10800045 DOI: 10.1186/s12933-024-02125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 01/07/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) increases the risk of coronary heart disease (CHD) by 2-4 fold, and is associated with endothelial dysfunction, dyslipidaemia, insulin resistance, and chronic hyperglycaemia. The aim of this investigation was to assess, by a multimarker mass spectrometry approach, the predictive role of circulating proteins as biomarkers of cardiovascular damage progression associated with diabetes mellitus. METHODS The study considered 34 patients with both T2DM and CHD, 31 patients with T2DM and without CHD, and 30 patients without diabetes with a diagnosis of CHD. Plasma samples of subjects were analysed through a multiplexed targeted liquid chromatography mass spectrometry (LC-MS)-based assay, namely Multiple Reaction Monitoring (MRM), allowing the simultaneous detection of peptides derived from a protein of interest. Gene Ontology (GO) Analysis was employed to identify enriched GO terms in the biological process, molecular function, or cellular component categories. Non-parametric multivariate methods were used to classify samples from patients and evaluate the relevance of the analysed proteins' panel. RESULTS A total of 81 proteins were successfully quantified in the human plasma samples. Gene Ontology analysis assessed terms related to blood microparticles, extracellular exosomes and collagen-containing extracellular matrix. Preliminary evaluation using analysis of variance (ANOVA) of the differences in the proteomic profile among patient groups identified 13 out of the 81 proteins as significantly different. Multivariate analysis, including cluster analysis and principal component analysis, identified relevant grouping of the 13 proteins. The first main cluster comprises apolipoprotein C-III, apolipoprotein C-II, apolipoprotein A-IV, retinol-binding protein 4, lysozyme C and cystatin-C; the second one includes, albeit with sub-grouping, alpha 2 macroglobulin, afamin, kininogen 1, vitronectin, vitamin K-dependent protein S, complement factor B and mannan-binding lectin serine protease 2. Receiver operating characteristic (ROC) curves obtained with the 13 selected proteins using a nominal logistic regression indicated a significant overall distinction (p < 0.001) among the three groups of subjects, with area under the ROC curve (AUC) ranging 0.91-0.97, and sensitivity and specificity ranging from 85 to 100%. CONCLUSIONS Targeted mass spectrometry approach indicated 13 multiple circulating proteins as possible biomarkers of cardiovascular damage progression associated with T2DM, with excellent classification results in terms of sensitivity and specificity.
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Affiliation(s)
| | - Cristina Banfi
- Centro Cardiologico Monzino, IRCCS, Milano, 20138, Italy.
| | - Eugenio Ragazzi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy.
| | - Erica Gianazza
- Centro Cardiologico Monzino, IRCCS, Milano, 20138, Italy
| | - Marco Munno
- Centro Cardiologico Monzino, IRCCS, Milano, 20138, Italy
| | - Massimo Carollo
- Department of Medicine - DIMED, University of Padova, Padova, Italy
| | - Pietro Traldi
- Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | | | - Giovanni Sartore
- Department of Medicine - DIMED, University of Padova, Padova, Italy
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Lee H, Kim M, Kim SH, Lee J, Lee TY, Rhee SJ, Roh S, Baik M, Jung HY, Kim H, Han DH, Ha K, Ahn YM, Kwon JS. Proteomic profiling in the progression of psychosis: Analysis of clinical high-risk, first episode psychosis, and healthy controls. J Psychiatr Res 2024; 169:264-271. [PMID: 38052137 DOI: 10.1016/j.jpsychires.2023.11.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND AND HYPOTHESIS Recent evidence has highlighted the benefits of early detection and treatment for better clinical outcomes in patients with psychosis. Biological markers of the disease have become a focal point of research. This study aimed to identify protein markers detectable in the early stages of psychosis and indicators of progression by comparing them with those of healthy controls (HC) and first episode psychosis (FEP). STUDY DESIGN The participants comprised 28 patients in the clinical high-risk (CHR) group, 49 patients with FEP, and 61 HCs aged 15-35 years. Blood samples were collected and analyzed using multiple reaction monitoring-mass spectrometry to measure the expression of 158 peptide targets. Data were adjusted for age, sex, and use of psychotropic drugs. STUDY RESULTS A total of 18 peptides (17 proteins) differed significantly among the groups. The protein PRDX2 was higher in the FEP group than in the CHR and HC groups and showed increased expression according to disease progression. The levels of six proteins were significantly higher in the FEP group than in the CHR group. Nine proteins differed significantly in the CHR group compared to the other groups. Sixteen proteins were significantly correlated with symptom severity. These proteins are primarily related to the coagulation cascade, inflammatory response, brain structure, and synaptic plasticity. CONCLUSIONS Our findings suggested that peripheral protein markers reflect disease progression in patients with psychosis. Further longitudinal research is needed to confirm these findings and to identify the specific roles of these markers in the pathogenesis of schizophrenia.
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Affiliation(s)
- Hyunju Lee
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Minah Kim
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Se Hyun Kim
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Junhee Lee
- Department of Psychiatry, Uijeongbu Eulji Medical Center, Uijeongbu, Republic of Korea.
| | - Tae Young Lee
- Department of Neuropsychiatry, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea.
| | - Sang Jin Rhee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Sungwon Roh
- Department of Neuropsychiatry, Hanyang University Hospital, Seoul, Republic of Korea.
| | - Myungjae Baik
- Department of Psychiatry, Kyung Hee University Medical Center, Kyung Hee University School of Medicine, Seoul, Republic of Korea.
| | - Hee Yeon Jung
- Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul, Republic of Korea; Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Hyeyoon Kim
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Do Hyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea; Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kyooseob Ha
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada; Department of Psychiatry, Lions Gate Hospital - Vancouver Coastal Health Authority, British Columbia, Canada.
| | - Yong Min Ahn
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea; Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea.
| | - Jun Soo Kwon
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea; Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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10
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Kemp J, Ladwig PM, Snyder MR. Alpha-1-Antitrypsin (A1AT) Proteotyping by LC-MS/MS. Methods Mol Biol 2024; 2750:95-106. [PMID: 38108970 DOI: 10.1007/978-1-0716-3605-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The diagnosis of alpha-1-antitrypsin (A1AT) deficiency is established by quantitation of protein concentration in serum (immunoassay) followed by determination of specific allelic variants by phenotyping (isoelectric focusing (IEF) gel electrophoresis) and/or allele-specific genotyping. Various phenotyping and genotyping methodologies are available, and each has their own advantages and disadvantages. As an alternative, mass spectrometry is emerging as a powerful tool in the identification and quantitation of proteins and peptides. The method described here, referred to as proteotyping, is a proteomic method using trypsin digestion and tandem mass spectrometry that detects the most common deficiency alleles, S and Z, associated with A1AT deficiency.This qualitative mass spectrometry method is based on the principle that the S and Z mutations lead to amino acid changes which result in a change in the mass of the A1AT protein. When the A1AT protein is proteolytically digested, multiple peptides are generated, two of which include the sites of the S and Z mutations, respectively. Peptides generated from wild-type A1AT (M alleles) differ in sequence and mass from peptides generated from the S and Z alleles at these two specific locations. The mass difference allows for differentiation of S and Z peptides, representing the deficiency alleles, from non-S and non-Z peptides, representing the wild-type alleles (M). Interpretation of the peptide patterns in conjunction with A1AT quantitation by immunoassay allows for an accurate assessment for the presence of deficiency alleles in the majority of patients.
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Affiliation(s)
- Jennifer Kemp
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paula M Ladwig
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Melissa R Snyder
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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11
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Sari R, Juho V, Katri S, Jaana UK. Determination of glyphosate and aminomethylphosphonic acid residues in Finnish soils by ultra-high performance liquid chromatography-tandem mass spectrometry. MethodsX 2023; 11:102397. [PMID: 37791013 PMCID: PMC10542195 DOI: 10.1016/j.mex.2023.102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023] Open
Abstract
Glyphosate [N-(phosphonomethyl) glycine] (GLY) adsorbs strongly in Finnish soils. A new method for GLY and its main degradation product, aminomethylphosphonic acid (AMPA) residues in clay soils (Protovertic Luvisol) was developed and validated. A new method was necessary because the previous one required laborious cleaning pre-treatments, and its recovery was quite poor (<40%-70%). In the new method, the earlier method's extraction solvent, 0.1 M potassium hydroxide (KOH), was replaced by more effective 0.6 M KOH. The old post-column high-performance liquid chromatography and fluorescence (HPLC-FLD) method was replaced by the ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method. Compounds were identified as their fluorenyl methyl chloroformate (FMOC) derivatives by a multiple reaction monitoring (MRM) technique and quantified by an internal standard method utilising multipoint matrix-matched calibration. Glufosinate-ammonium (GLUF) was used to monitor the effectiveness of extraction with good recovery (80-119%). All calibration curves were found to be linear (R2 ≥ 0.98) in the studied calibration range (0.01-3.31 mg kg-1 in fresh soil). The repeatability and reproducibility were 25% and 28% for GLY, and 20% and 24% for AMPA in real research soil samples. The method was effective throughout the calibration range in all the studied Finnish agricultural soils.•An improved method was created to analyse glyphosate (GLY) and AMPA in Finnish clay soil.•The challenge caused by strong GLY adsorption on soil was solved by using multipoint matrix-matched calibration curve samples which were prepared identically with the research samples.•The method performed well in all tested clay, loam and sandy loam soils.
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Affiliation(s)
- Rämö Sari
- Natural Resources Institute Finland (Luke), Myllytie 1, Jokioinen 31600, Finland
| | - Välimäki Juho
- MTT Agrifood Research, Finland
- current: KVVY Tutkimus Oy, Patamäenkatu 24, Tampere 33900, Finland
| | - Siimes Katri
- Finnish Environmental Institute (Syke), Latokartanonkaari 11, Helsinki 00790, Finland
| | - Uusi-Kämppä Jaana
- Natural Resources Institute Finland (Luke), Tietotie 4, Jokioinen 31600, Finland
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12
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Cao X, Tang X, Feng C, Lin J, Zhang H, Liu Q, Zheng Q, Zhuang H, Liu X, Li H, Khan NU, Shen L. A Systematic Investigation of Complement and Coagulation-Related Protein in Autism Spectrum Disorder Using Multiple Reaction Monitoring Technology. Neurosci Bull 2023; 39:1623-1637. [PMID: 37031449 PMCID: PMC10603015 DOI: 10.1007/s12264-023-01055-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/02/2023] [Indexed: 04/10/2023] Open
Abstract
Autism spectrum disorder (ASD) is one of the common neurodevelopmental disorders in children. Its etiology and pathogenesis are poorly understood. Previous studies have suggested potential changes in the complement and coagulation pathways in individuals with ASD. In this study, using multiple reactions monitoring proteomic technology, 16 of the 33 proteins involved in this pathway were identified as differentially-expressed proteins in plasma between children with ASD and controls. Among them, CFHR3, C4BPB, C4BPA, CFH, C9, SERPIND1, C8A, F9, and F11 were found to be altered in the plasma of children with ASD for the first time. SERPIND1 expression was positively correlated with the CARS score. Using the machine learning method, we obtained a panel composed of 12 differentially-expressed proteins with diagnostic potential for ASD. We also reviewed the proteins changed in this pathway in the brain and blood of patients with ASD. The complement and coagulation pathways may be activated in the peripheral blood of children with ASD and play a key role in the pathogenesis of ASD.
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Affiliation(s)
- Xueshan Cao
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xiaoxiao Tang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Chengyun Feng
- Maternal and Child Health Hospital of Baoan, Shenzhen, 518100, China
| | - Jing Lin
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Huajie Zhang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Qiong Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Qihong Zheng
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Hongbin Zhuang
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xukun Liu
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Haiying Li
- Department of Endocrinology, Guiyang First People's Hospital, Guiyang, 550002, China
| | - Naseer Ullah Khan
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Liming Shen
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China.
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, Shenzhen, 518060, China.
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13
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Wang Q, Xu PJ, Mesaros C. Ultrasensitive quantification of estrogens in serum and plasma by liquid chromatography-tandem mass spectrometry. Methods Enzymol 2023; 689:433-452. [PMID: 37802582 DOI: 10.1016/bs.mie.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Stable isotope dilution (SID) methodology coupled with liquid chromatography-tandem mass spectrometry (LC-MS) is rapidly becoming the gold standard for measuring estrogens in serum and plasma due to improved specificity, high accuracy, and the ability to conduct a more comprehensive analysis. A general consideration of the problems associated with measuring estrogens and two detailed derivatization methods are described in this chapter. These methods quantify estrogens and their metabolites in serum and plasma samples using this state-of-art technology, which is applicable to the routine clinical laboratory.
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Affiliation(s)
- Qingqing Wang
- Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States
| | - Peining Jimmy Xu
- Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States
| | - Clementina Mesaros
- Center for Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United States.
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14
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Chan WH, Yau LF, Meng XY, Chan KM, Jiang ZH, Wang JR. Robust quantitation of gangliosides and sulfatides in human brain using UHPLC-MRM-MS: Method development and application in Alzheimer's disease. Talanta 2023; 256:124264. [PMID: 36689895 DOI: 10.1016/j.talanta.2023.124264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Gangliosides (GAs) and sulfatides (STs) are acidic glycosphingolipids that are particularly abundant in the nervous system and are closely related to aging and neurodegenerative disorders. To explore their roles in brain diseases, in-depth molecular profiling, including structural variations of sphingoid backbone, fatty acyl group, and sugar chain of GAs and STs was performed. A total of 210 GAs and 38 STs were characterized in the inferior frontal gyrus (IFG) of human brain, with 90 GAs discovered in brain tissues for the first time. Influential MS parameters for detecting GAs and STs in multiple reaction monitoring (MRM) mode were systematically examined and optimized to minimize in-source fragmentation, resulting in remarkable signal intensity enhancement for GAs and STs, especially for polysialylated species. To eliminate analytical variations, isotopic interference-free internal standards were prepared by simple and fast reduction reaction. The final established method facilitated the simultaneous quantitation of 184 GAs and 30 STs from 25 subtypes, which represents the highest number of GAs quantitated among all quantitation methods recorded in literature so far. The method was further validated and applied to reveal the aberrant change of GAs and STs in the IFG of 12 Alzheimer's disease (AD) patients. Four GAs exhibited high classification capacity for AD (AUC ≥0.80) and were thereby considered the most promising signatures for AD. These findings suggested the close correlation between GAs and the pathogenesis of AD, highlighting the achievements of our robust method for investigating the roles of GAs and STs in various physiological states and diseases.
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Affiliation(s)
- Wai-Him Chan
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, 999078, Macao, China
| | - Lee-Fong Yau
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, 999078, Macao, China
| | - Xiong-Yu Meng
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, 999078, Macao, China
| | - Ka-Man Chan
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, 999078, Macao, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, 999078, Macao, China
| | - Jing-Rong Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, 999078, Macao, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510000, China.
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15
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Brookhart A, Arora M, McCullagh M, Wilson ID, Plumb RS, Vissers JP, Tanna N. Understanding mobile phase buffer composition and chemical structure effects on electrospray ionization mass spectrometry response. J Chromatogr A 2023; 1696:463966. [PMID: 37054638 DOI: 10.1016/j.chroma.2023.463966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Mobile phase selection is of critical importance in liquid chromatography - mass spectrometry (LC-MS) based studies, since it affects retention, chromatographic selectivity, ionization, limits of detection and quantification, and linear dynamic range. Generalized LC-MS mobile phase selection criteria, suitable for a broad class of chemical compounds, do not exist thus far. Here we have performed a large-scale qualitative assessment of the effect of solvent composition used for reversed-phase LC separations on electrospray ionization (ESI) response for 240 small molecular weight drugs, representing various chemical compound classes. Of these 240 analytes 224 were detectable using ESI. The main chemical structural features affecting ESI response were found to all be surface area or surface charge-related. Mobile phase composition was found to be less differentiating, although for some compounds a pH effect was noted. Unsurprisingly, chemical structure was found to be the dominant factor for ESI response for the majority of the investigated analytes, representing about 85% of the replicating detectable complement of the sample data set. A weak correlation between ESI response and structure complexity was observed. Solvents based on isopropanol, and those containing phosphoric or di- and trifluoracetic acids, performed relatively poorly in terms of chromatographic or ESI response, whilst the best performing 'generic' LC solvents were based on methanol, acetonitrile using formic acid and ammonium acetate as buffer components, consistent with current practice in many laboratories.
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Affiliation(s)
- Allison Brookhart
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA
| | - Mahika Arora
- Manning College of Information and Computer Sciences, University of Massachusetts Amherst, MA
| | | | - Ian D Wilson
- Computational & Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, United Kingdom
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16
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Hu A, Zhang J, Shen H. Progress in Targeted Mass Spectrometry (Parallel Accumulation-Serial Fragmentation) and Its Application in Plasma/Serum Proteomics. Methods Mol Biol 2023; 2628:339-352. [PMID: 36781796 DOI: 10.1007/978-1-0716-2978-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Targeted mass spectrometry using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) has been commonly used for protein biomarker validation in plasma, serum, or other clinically relevant specimens due to its high specificity, selectivity, and multiplexing capability compared with immunoassays. As the emerging mode termed parallel accumulation-serial fragmentation (prmPASEF) significantly improved analyte throughput (100-1000), sensitivity (attomole level), and acquisition speed, it promises to broaden the application of targeted mass spectrometry to simultaneous biomarker discovery and validation with high accuracy. Here, we summarize the general approach of the MRM and PRM techniques used for serum/plasma proteomics and describe a detailed step-by-step procedure for the development of MRM/PRM assays for secreted proteins.
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Affiliation(s)
- Anqi Hu
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China
| | - Jiayi Zhang
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China
| | - Huali Shen
- Institutes of Biomedical Sciences and Minhang Hospital, Fudan University, Shanghai, China.
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17
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Wang YZ, Mei PC, Bai PR, An N, He JG, Wang J, Zhu QF, Feng YQ. A strategy for screening and identification of new amino acid-conjugated bile acids with high coverage by liquid chromatography-mass spectrometry. Anal Chim Acta 2023; 1239:340691. [PMID: 36628759 DOI: 10.1016/j.aca.2022.340691] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
Bile acids (BAs) are a class of vital gut microbiota-host cometabolites, and they play an important role in maintaining gut microbiota-host metabolic homeostasis. Very recently, a new mechanism of BA anabolic metabolism mediated by gut microbiota (BA-amino acid conjugation) has been revealed, which provides a perspective for the research on BA metabolism and gut metabolome. In this study, we established a polarity-switching multiple reaction monitoring mass spectrometry-based screening method to mine amino acid-conjugated bile acids (AA-BAs) derived from host-gut microbiota co-metabolism. In addition, a retention time-based annotation strategy was further proposed to identify the AA-BA isomers and epimers. Using the developed methods, we successfully screened 118 AA-BA conjugates from mouse and human feces, 28 of them were confirmed by standards, and 62 putatively identified based on their predicted retention times. Moreover, we observed that the levels of most AA-BAs were significantly downregulated in the feces of chronic sleep deprivation mice, suggesting that the AA-BA metabolism was closely related to the physiological state of the host.
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18
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Newman LA, Useckaite Z, Wu T, Sorich MJ, Rowland A. Analysis of Extracellular Vesicle and Contaminant Markers in Blood Derivatives Using Multiple Reaction Monitoring. Methods Mol Biol 2023; 2628:301-320. [PMID: 36781794 DOI: 10.1007/978-1-0716-2978-9_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Extracellular vesicles (EVs) are naturally occurring membranous particles that can be isolated from blood and other biofluids. EVs have drawn considerable attention for their potential as a minimally invasive biomarker source for a range of conditions, based on tissue-specific expression of proteins and other molecular information. To promote robust characterization of EV isolates, the International Society for Extracellular Vesicles (ISEV) has established consensus minimal requirements for the study of extracellular vesicles (MISEV) reporting guidelines. A core element of MISEV guidance is the recommendation for the analysis of protein markers in samples, including positive EV-associated markers and negative contaminant markers based on commonly co-isolated components of the sample matrix. Furthermore, there is growing interest in circulating EVs enriched for tissue-specific origin, and in this context, the degree of nontarget EV "contamination" (e.g., EVs derived from blood cells) may inform assessment of sample purity. The increasing application of EVs as a liquid biopsy for clinical applications requires a high-throughput multiplexed approach that enables analysis of protein markers from small volumes of starting material, ideally utilizing the same platform for measuring biomarkers of interest. To this end, targeted liquid chromatography mass spectrometry using multiple reaction monitoring (LC-MRM-MS) is a key platform for the quantitative assessment of target proteins within EV samples. Here we describe a protocol for the isolation of EVs from blood and parallel analytical methods targeting general EV markers and blood cell-derived EV markers, along with guidance of best practice for sample collection and processing.
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Affiliation(s)
- Lauren A Newman
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Zivile Useckaite
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Ting Wu
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Michael J Sorich
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Andrew Rowland
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
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19
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Abstract
Extraction and quantification of endocannabinoids from biological tissues is essential to unravel their changes under physiological and pathophysiological conditions. We describe here an analytical protocol for the extraction of endocannabinoids, anandamide (archidonoyl ethanolamide, AEA) and 2-arachidonoyl glycerol (2-AG), and endocannabinoid-like lipids such as palmitoyl ethanolamide (PEA) and oleoyl ethanolamide (OEA), as well as arachidonic acid (AA) from biological tissues using liquid-liquid extraction method and simultaneous quantification by liquid chromatography multiple reaction monitoring (LC/MRM).
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Affiliation(s)
- Claudia Schwitter
- Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Beat Lutz
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany.
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20
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Roper SM, Weindel AL, Dietzen DJ. Comprehensive Determination of Amino Acids for Diagnosis of Inborn Errors of Metabolism. Methods Mol Biol 2022; 2546:55-64. [PMID: 36127578 DOI: 10.1007/978-1-0716-2565-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Analysis of clinically relevant amino acids using ion exchange chromatography coupled to photometric/fluorescent detection has been an indispensable component in the detection of inborn errors of metabolism for six decades. Detection of amino acids using mass spectrometry offers advantages in speed and analytic specificity. Employing methanol extraction and controlled butylation, C8 reversed-phase chromatography, and MS/MS detection, 32 amino acids are quantified in 20 min with clinically appropriate imprecision in plasma, urine, and cerebrospinal fluid (CSF). Quantitation is linear to 2500 μM, and limits of detection are at least 1.0 μM. Important isobaric amino acids are distinguished by chromatography or by unique patterns of fragmentation following collision-induced dissociation (CID). The technique employs commercially available reagents and may be expanded and customized for specific clinical or research settings.
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21
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Luque-Córdoba D, Calderón-Santiago M, Priego-Capote F. Combining data acquisition modes in liquid-chromatography-tandem mass spectrometry for comprehensive determination of acylcarnitines in human serum. Metabolomics 2022; 18:59. [PMID: 35859020 PMCID: PMC9300566 DOI: 10.1007/s11306-022-01916-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022]
Abstract
Acylcarnitines (ACs) are metabolites involved in fatty acid β-oxidation and organic acid metabolism. Metabolic disorders associated to these two processes can be evaluated by determining the complete profile of ACs. In this research, we present an overall strategy for identification, confirmation, and quantitative determination of acylcarnitines in human serum. By this strategy we identified the presence of 47 ACs from C2 to C24 with detection of the unsaturation degree by application of a data-independent acquisition (DIA) liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. Complementary, quantitative determination of ACs is based on a high-throughput and fully automated method consisting of solid-phase extraction on-line coupled to LC-MS/MS in data-dependent acquisition (DDA) to improve analytical features avoiding the errors associated to sample processing. Quantitation limits were at pg mL-1 level, the intra-day and between-day variability were below 15-20%, respectively; and the accuracy, expressed as bias, was always within ± 25%. The proposed method was tested with 40 human volunteers to determine the relative concentration of ACs in serum and identify predominant forms. Significant differences were detected by comparing the ACs profile of obese versus non-obese individuals.
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Affiliation(s)
- D Luque-Córdoba
- Department of Analytical Chemistry, University of Córdoba, Annex Marie Curie Building, Campus of Rabanales, Córdoba, Spain
- Nanochemistry University Institute (IUNAN), University of Córdoba, Campus of Rabanales, Córdoba, Spain
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain
- Consortium for Biomedical Research in Frailty & Healthy Ageing, Carlos III Institute of Health, CIBERFES, Madrid, Spain
| | - M Calderón-Santiago
- Department of Analytical Chemistry, University of Córdoba, Annex Marie Curie Building, Campus of Rabanales, Córdoba, Spain
- Nanochemistry University Institute (IUNAN), University of Córdoba, Campus of Rabanales, Córdoba, Spain
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain
- Consortium for Biomedical Research in Frailty & Healthy Ageing, Carlos III Institute of Health, CIBERFES, Madrid, Spain
| | - F Priego-Capote
- Department of Analytical Chemistry, University of Córdoba, Annex Marie Curie Building, Campus of Rabanales, Córdoba, Spain.
- Nanochemistry University Institute (IUNAN), University of Córdoba, Campus of Rabanales, Córdoba, Spain.
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain.
- Consortium for Biomedical Research in Frailty & Healthy Ageing, Carlos III Institute of Health, CIBERFES, Madrid, Spain.
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22
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Li XY, Fu YJ, Fu YF, Wei W, Xu C, Yuan XH, Gu CB. Simultaneous quantification of fourteen characteristic active compounds in Eucommia ulmoides Oliver and its tea product by ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-QqQ-MS/MS). Food Chem 2022; 389:133106. [PMID: 35504080 DOI: 10.1016/j.foodchem.2022.133106] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 11/04/2022]
Abstract
Various kinds of bioactive compounds contribute to versatile health-promoting properties of Eucommia ulmoides Oliver (E. ulmoides). In present study, we developed a UPLC-QqQ-MS/MS method for simultaneous quantification of fourteen characteristic active compounds, including 3 lignans, 4 iridoids, 3 flavonoids and 4 phenolics in E. ulmoides and its tea product for the first time. The running time of the method is 6.5 min. It has good linearity, sensitivity, precision, accuracy, and stability. Using this high-throughput method, the distributions of fourteen characteristic active compounds in E. ulmoides and its tea product were clarified. Also, it was found that E. ulmoides tea exhibited superiority in contents of chlorogenic acid as compared with natural resources. Overall, the study provided a rapid, reliable, and efficient analysis method, which could be applied for the quality evaluation of E. ulmoides natural resources and their relative products in the field of food and medicine.
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Affiliation(s)
- Xin-Yue Li
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China; Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, Harbin 150040, PR China
| | - Yu-Jie Fu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Forestry, Beijing Forestry University, Beijing 100083, PR China
| | - Yue-Feng Fu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China; Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, Harbin 150040, PR China
| | - Wei Wei
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China; Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, Harbin 150040, PR China
| | - Cheng Xu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China; Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, Harbin 150040, PR China
| | - Xiao-Han Yuan
- Life Science and Biotechnique Research Center, Northeast Agricultural University, Harbin 150030, PR China
| | - Cheng-Bo Gu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China; Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, Harbin 150040, PR China.
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23
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Grabowska K, Macur K, Zieschang S, Zaman L, Haverland N, Schissel A, Morsey B, Fox HS, Ciborowski P. HIV-1 and methamphetamine alter galectins -1, -3, and -9 in human monocyte-derived macrophages. J Neurovirol 2022; 28:99-112. [PMID: 35175539 PMCID: PMC9076712 DOI: 10.1007/s13365-021-01025-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/30/2021] [Accepted: 10/27/2021] [Indexed: 12/05/2022]
Abstract
Macrophages are key elements of the innate immune system. Their HIV-1 infection is a complex process that involves multiple interacting factors and various steps and is further altered by exposure of infected cells to methamphetamine (Meth), a common drug of abuse in people living with HIV. This is reflected by dynamic changes in the intracellular and secreted proteomes of these cells. Quantification of these changes poses a challenge for experimental design and associated analytics. In this study, we measured the effect of Meth on expression of intracellular and secreted galectins-1, -3, and -9 in HIV-1 infected human monocyte-derived macrophages (hMDM) using SWATH-MS, which was further followed by MRM targeted mass spectrometry validation. Cells were exposed to Meth either prior to or after infection. Our results are the first to perform comprehensive quantifications of galectins in primary hMDM cells during HIV-1 infection and Meth exposure a building foundation for future studies on the molecular mechanisms underlying cellular pathology of hMDM resulting from viral infection and a drug of abuse—Meth.
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Affiliation(s)
- Kinga Grabowska
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.,Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Katarzyna Macur
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.,Core Facility Laboratories, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Sarah Zieschang
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lubaba Zaman
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nicole Haverland
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Andrew Schissel
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Brenda Morsey
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, School of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.
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24
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Guerrero L, Paradela A, Corrales FJ. Development of a Standardized MRM Method for the Quantification of One Carbon Metabolism Enzymes. Methods Mol Biol 2022; 2420:159-75. [PMID: 34905173 DOI: 10.1007/978-1-0716-1936-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
One-carbon metabolism (1CM) plays a central role in liver physiology, being the source of essential metabolites such as S-adenosylmethionine, the main alkylating agent in living cells, and glutathione, their most important nonenzymatic antioxidant defense. Impairment of 1CM in hepatocytes is a recognized factor associated to chronic liver disorders and hepatocellular carcinoma. With this in mind, we have proposed the concept of functional biomarker referring to a cellular pathway that can be systematically monitored as indicative of a particular physiological or pathological condition. Here we describe a targeted mass spectrometry (MRM) protocol to simultaneously quantify 13 1CM enzymes in liver tissue specimens.
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25
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Liu Q, Bi Q, Zhang J, Qin W, Yi S, Hu Q, Sun J, Ji S, Tan N. A rapid and simple signature peptides-based method for species authentication of three main commercial Pheretima. J Proteomics 2021; 255:104456. [PMID: 34922013 DOI: 10.1016/j.jprot.2021.104456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 11/18/2021] [Accepted: 12/06/2021] [Indexed: 10/19/2022]
Abstract
Pheretima with various activities is a commonly used animal-derived traditional medicine in Asia countries. However, almost half of them are non-pharmacopoeia species in the market due to the similar morphological characteristics between medicinal and non-medicinal species. This study aims to establish an effective method based on signature peptides for species authentication of three main commercial Pheretima, including two major Pheretima species (Amynthas aspergillum, Metaphire vulgaris) and one main adulteration (Metaphire magna). Firstly, the species of 52 batches of commercial Pheretima were authenticated based on DNA barcodes. Secondly, proteomic analysis was performed for protein characterization of three main commercial Pheretima. Furthermore, their signature peptides were screened and validated using ultra-high performance liquid chromatography coupled with mass spectrometry (UPLC-MS/MS) in multiple reaction monitoring (MRM) mode. Moreover, a simplified sample processing method was developed. Finally, large quantities of commercial Pheretima samples were analyzed for further verifying the feasibility of the signature peptides-based method. The result showed that the established method had a great application potential for authenticity identification of commercial Pheretima. SIGNIFICANCE: The authenticity assessment of medicinal materials is a main issue in the quality control process as deceptive practices could imply severe health risks. In this study, a rapid and simple method based on signature peptides was established for species authentication of three main commercial Pheretima, which can be an effective alternative to complex DNA barcoding and difficult morphological identification, and provided a reference for improvement of Pheretima quality standards.
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Affiliation(s)
- Qiao Liu
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Qirui Bi
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingxian Zhang
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, 1500 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Weiwei Qin
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Shanyong Yi
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Qing Hu
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, 1500 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Jian Sun
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, 1500 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Shen Ji
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, 1500 Zhangheng Road, Shanghai 201203, People's Republic of China.
| | - Ninghua Tan
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China.
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26
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Nguyen A, Wang T, Turko IV. Quantitative proteomic analysis for evaluating affinity isolation of extracellular vesicles. J Proteomics 2021; 249:104359. [PMID: 34454076 DOI: 10.1016/j.jprot.2021.104359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022]
Abstract
Absolute quantification with mass spectrometry and isotope labeled internal standards has found broad applications in biomedical research. In the present research, it was used for developing and evaluating a new affinity-based approach to isolate extracellular vesicles (EVs) from human plasma. First, a phage display peptide library was screened against EVs as a bait and absolute quantification of multiple proteins helped to select the best bait available. Then, absolute quantification was used to evaluate the efficiency of affinity chromatography on peptide-Sepharose. In summary, we have demonstrated that peptides with affinity to EVs selected from phage library screening can be valuable ligands for EVs isolation. SIGNIFICANCE: Extracellular vesicles (EVs) have an important role in intercellular communication for all cell types. This makes EVs a promising new type of therapeutics capable to deliver drugs to specific sites with no off-target side effects. However, their isolation, and correct assignment of their biological function and properties remains an obscure field of research. In this study, we proposed to use MRM quantitation of a pattern of EVs and non-EVs proteins to develop a purification protocol based on affinity peptides selected from phage library screening. MRM quantification of EVs proteins can also help in identifying those that are subpopulation specific markers for further target-specific isolation.
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27
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Liu Q, Bi Q, Tan N. Authentication of three main commercial Pheretima based on amino acids analysis. Amino Acids 2021; 53:1729-38. [PMID: 34613459 DOI: 10.1007/s00726-021-03043-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/15/2020] [Indexed: 10/20/2022]
Abstract
Pheretima has been used as an animal-derived traditional Chinese medicine for thousands of years in Asian countries due to its multi-activities. However, more than half of the commercial Pheretima are adulterants according to the previous research. Besides, the standards of Pheretima are still inadequate in the identification of Pheretima species. In this study, an amino acids (AAs) analytical method established based on the ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-QqQ-MS) in multiple reaction monitoring (MRM) mode through derivatization with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) was used for qualitative and quantitative analysis of the total AAs of three main commercial Pheretima (two major Pheretima species, Amynthas aspergillum, Metaphire vulgaris, and one main counterfeit, M. magna). As a result, 16 AAs were detected and quantitated in their hydrolyzed samples. Then, multivariate statistical analysis was applied to distinguish the three commercial Pheretima based on their AAs level. Finally, four AAs (Thr, Glu, Asp, and Arg) were screened as species-differential AAs, which may be used as chemical markers to distinguish the three commercial Pheretima. This study deeply described the outline of AAs in Pheretima and offered a good reference for its species authentication.
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28
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Chen R, Brown HM, Cooks RG. Metabolic profiles of human brain parenchyma and glioma for rapid tissue diagnosis by targeted desorption electrospray ionization mass spectrometry. Anal Bioanal Chem 2021; 413:6213-6224. [PMID: 34373931 PMCID: PMC8522078 DOI: 10.1007/s00216-021-03593-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022]
Abstract
Desorption electrospray ionization mass spectrometry (DESI-MS) is well suited for intraoperative tissue analysis since it requires little sample preparation and offers rapid and sensitive molecular diagnostics. Currently, intraoperative assessment of the tumor cell percentage of glioma biopsies can be made by measuring a single metabolite, N-acetylaspartate (NAA). The inclusion of additional biomarkers will likely improve the accuracy when distinguishing brain parenchyma from glioma by DESI-MS. To explore this possibility, mass spectra were recorded for extracts from 32 unmodified human brain samples with known pathology. Statistical analysis of data obtained from full-scan and multiple reaction monitoring (MRM) profiles identified discriminatory metabolites, namely gamma-aminobutyric acid (GABA), creatine, glutamic acid, carnitine, and hexane-1,2,3,4,5,6-hexol (abbreviated as hexol), as well as the established biomarker NAA. Brain parenchyma was readily differentiated from glioma based on these metabolites as measured both in full-scan mass spectra and by the intensities of their characteristic MRM transitions. New DESI-MS methods (5 min acquisition using full scans and MS/MS), developed to measure ion abundance ratios among these metabolites, were tested using smears of 29 brain samples. Ion abundance ratios based on signals for GABA, creatine, carnitine, and hexol all had sensitivities > 90%, specificities > 80%, and accuracies > 85%. Prospectively, the implementation of diagnostic ion abundance ratios should strengthen the discriminatory power of individual biomarkers and enhance method robustness against signal fluctuations, resulting in an improved DESI-MS method of glioma diagnosis.
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Affiliation(s)
- Rong Chen
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Hannah Marie Brown
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA.
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29
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Snyman T, Crowther NJ. The Detection of Toxic Compounds in Extracts of Callilepis laureola (Oxeye Daisy) and Senecio latifolius (Ragwort) by Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS/MS). Methods Mol Biol 2022; 2343:381-93. [PMID: 34473339 DOI: 10.1007/978-1-0716-1558-4_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Methods used for the detection of toxic components of Callilepis laureola and Senecio latifolius have ranged from the use of thin-layer chromatography, spectrophotometry, and immunoassay to gas chromatography with mass spectrometry. However, each of these techniques has a number of drawbacks. In this chapter, we will describe a solid-phase extraction technique, which allows for the detection and quantitation of the toxins atractyloside and retrorsine in each plant extract using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). This methodology offers high specificity and sensitivity and the ability to identify a broad range of analytes.
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30
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Prieto-Santiago V, Cavia MDM, Barba FJ, Alonso-Torre SR, Carrillo C. Multiple reaction monitoring for identification and quantification of oligosaccharides in legumes using a triple quadrupole mass spectrometer. Food Chem 2021; 368:130761. [PMID: 34392119 DOI: 10.1016/j.foodchem.2021.130761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 06/05/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022]
Abstract
Raffinose family oligosaccharides are non-digestible compounds considered as dietary prebiotics with health-related properties. Hence, it is important to develop highly specific methods for their determination. An analytical method is developed in this study for oligosaccharide identification and quantification using liquid chromatography-tandem mass spectrometry equipped with a triple quadrupole analyser operating in Multiple Reaction Monitoring mode. Raffinose, stachyose and verbascose are separated in a 10-minute run and the method is validated over a broad concentration range, showing good linearity, accuracy, precision and high sensitivity. A low-cost, short eco-friendly procedure for oligosaccharide extraction from legumes, with a high recovery rate extraction, good repeatability and reproducibility is also proposed. No plant-matrix effects were demonstrated. The method applied to the screening of 28 different legumes revealed species-related traits for oligosaccharide distribution, highlighting Pisum sativum (9.22 g/100 g) as the richest source of these prebiotics and its suitability as a functional food ingredient.
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Affiliation(s)
| | - María Del Mar Cavia
- Nutrición y Bromatología, Facultad de Ciencias, Universidad de Burgos, E-09001 Burgos, Spain
| | - Francisco J Barba
- Nutrition and Food Science Area, Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, Universitat de València, Avda Vicent Andrés Estellés, s/n. 46100, Burjassot, València, Spain
| | - Sara R Alonso-Torre
- Nutrición y Bromatología, Facultad de Ciencias, Universidad de Burgos, E-09001 Burgos, Spain
| | - Celia Carrillo
- Nutrición y Bromatología, Facultad de Ciencias, Universidad de Burgos, E-09001 Burgos, Spain.
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31
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Wang J, Xu D, Ni Z, Yu C, Wang J, Wu Q, Di L, Cheng H, Duan J, Zhou J, Ma H. Analyzing liver protein-bound DMA V by using size exclusion and ion exchange HPLC combined with ICP-MS and MRM mode in rats exposed to AS4S4. Talanta 2021; 234:122714. [PMID: 34364506 DOI: 10.1016/j.talanta.2021.122714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/06/2021] [Accepted: 07/11/2021] [Indexed: 12/22/2022]
Abstract
Long-term exposure to high levels of arsenic (As) will result in damage to organs. Compared with free arsenic, protein-bound arsenic are more difficult to be excreted from the bodies due to their complexation with biological macromolecules. We developed a method of size exclusion chromatography (SEC) and ion exchange chromatography (IEC) combined with inductively coupled plasma-mass spectrometry (ICP-MS) and multiple reaction monitoring (MRM) mode, which was used to determine bound-arsenic species. DMAV was identified as bound arsenic species in rat livers after As4S4 overexposure. Subsequent proteomics analysis showed the potential binding partners included hemoglobin, glutathione S-transferases, superoxide dismutase [Cu-Zn] & [Mn], thiosulfate sulfurtransferase, and metallothionein-2. The method developed here was sensitive, repeatable, and conducive to arsenic analysis, especially for toxicity evaluation of arsenic-containing substances in vivo.
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Affiliation(s)
- Jiaojiao Wang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Dihui Xu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Chengli Yu
- Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiajia Wang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qinan Wu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Liuqing Di
- Jiangsu Provincial TCM Engineering Technology Research Center of High Efficient Drug Delivery System (DDS), Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Haibo Cheng
- Translational Medicine Research Center, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Jing Zhou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Hongyue Ma
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
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32
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Jenkins LM, Nam JW, Evans BS, Allen DK. Quantification of Acyl-Acyl Carrier Proteins for Fatty Acid Synthesis Using LC-MS/MS. Methods Mol Biol 2021; 2295:219-47. [PMID: 34047980 DOI: 10.1007/978-1-0716-1362-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The fatty acid biosynthetic cycle is predicated on an acyl carrier protein (ACP) scaffold where two carbon acetyl groups are added in a chain elongation process through a series of repeated enzymatic steps. The chain extension is terminated by hydrolysis with a thioesterase or direct transfer of the acyl group to a glycerophospholipid by an acyltransferase. Methods for analysis of the concentrations of acyl chains attached to ACPs are lacking but would be informative for studies in lipid metabolism. We describe a method to profile and quantify the levels of acyl-ACPs in plants, bacteria and mitochondria of animals and fungi that represent Type II fatty acid biosynthetic systems. ACPs of Type II systems have a highly conserved Asp-Ser-Leu-Asp (DSLD) amino acid sequence at the attachment site for 4'-phosphopantetheinyl arm carrying the acyl chain. Three amino acids of the conserved sequence can be cleaved away from the remainder of the protein using an aspartyl protease. Thus, partially purified protein can be enzymatically hydrolyzed to produce an acyl chain linked to a tripeptide via the 4'-phosphopantetheinyl group. After ionization and fragmentation, the corresponding fragment ion is detected by a triple quadrupole mass spectrometer using a multiple reaction monitoring method. 15N isotopically labeled acyl-ACPs generated in high amounts are used with an isotope dilution strategy to quantify the absolute levels of each acyl group attached to the acyl carrier protein scaffold.
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Abstract
The acyl-CoA pool is pivotal in cellular metabolism. The ability to provide reliable estimates of acyl-CoA abundance and distribution between molecular species in plant tissues and microalgae is essential to our understanding of lipid metabolism and acyl exchange. Acyl-CoAs are typically found in low abundance and require specific methods for extraction, separation and detection. Here we describe methods for acyl-CoA extraction and measurement in plant tissues and microalgae, with a focus on liquid chromatography hyphenated to detection techniques including ultraviolet (UV), fluorescence and mass spectrometry (MS). We address the resolution of isobaric species and the selection of columns needed to achieve this, including the analysis of branched chain acyl-CoA thioesters. For MS analyses, we describe diagnostic ions for the identification of acyl-CoA species and how these can be used for both discovery of new species (data dependent acquisition) and routine quantitation (triple quadrupole MS with multiple reaction monitoring).
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Affiliation(s)
- Richard P Haslam
- Department of Plant Science, Rothamsted Research, Harpenden, UK.
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34
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Goh EXY, Guan XL. Targeted Lipidomics of Drosophila melanogaster During Development. Methods Mol Biol 2021; 2306:187-213. [PMID: 33954948 DOI: 10.1007/978-1-0716-1410-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Lipids play critical roles in developmental processes, and alterations in lipid metabolism are linked to a wide range of human diseases, including neurodegeneration, cancer, metabolic diseases, and microbial infections. Drosophila melanogaster, more commonly known as the fruit fly, is a powerful organism for developmental biology and human disease research. We have previously developed a comprehensive biochemical tool, based on liquid chromatography-mass spectrometry (LC-MS), to probe the dynamics of lipid remodeling during D. melanogaster development. This chapter introduces a step-by-step protocol for extracting and analyzing lipids across all developmental stages (embryo, larvae, pupa, and adult) of D. melanogaster. The targeted semi-quantitative approach offers a comprehensive coverage of more than 400 lipid species spanning the lipid classes, glycerophospholipids, sphingolipids, triacylglycerols, and sterols.
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Affiliation(s)
- Esther Xue Yi Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
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35
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Li M, Yang X, Sun L, Qing Y, Hu X, Jiang J, Wang D, Cui G, Gao Y, Zhang E, Zhang J, Yang Y, Wan C. Decreased serum apolipoprotein A4 as a potential peripheral biomarker for patients with schizophrenia. J Psychiatr Res 2021; 137:14-21. [PMID: 33640722 DOI: 10.1016/j.jpsychires.2021.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/15/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Recent evidence supports an association between lipid metabolism dysfunction and the pathology of schizophrenia which has led to the search for peripheral blood-based biomarkers. The purpose of this study was to investigate the proteins involved in lipid metabolism (especially apolipoprotein) and to explore their potential as biomarkers for schizophrenia. Using multiple reaction monitoring mass spectrometry (MRM-MS), we quantified 22 proteins in serum samples of 109 healthy controls (HCs) and 111 patients with schizophrenia (SCZ), who were divided into discovery and validation sets. We found serum apolipoprotein A4 (ApoA4) to be significantly decreased in SCZ patients compared to HCs (p=1.61E-05). Moreover, the serum ApoA4 level served as an effective diagnostic tool, achieving area under the receiver operating characteristic curves (AUROC) of 0.840 in the discovery set and 0.791 in the validation set. Additionally, apolipoprotein F (ApoF), angiotensinogen (AGT), and alpha1-antichymotrypsin (ACT) levels were significantly higher in patients with schizophrenia than in healthy controls. These proteins combined with ApoA4, provided higher diagnostic accuracy for schizophrenia in the discovery set (AUROC=0.901) and in the validation set (AUROC=0.879). Our results suggest that the serum level of ApoA4 is a novel potential biomarker for schizophrenia. The proteins identified in this study expand the pool of biomarker candidates for schizophrenia and may be linked to the underlying mechanism of the disease.
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Affiliation(s)
- Minghui Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xuhan Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Liya Sun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Qing
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowen Hu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Jiang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Dandan Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Gaoping Cui
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Gao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - En Zhang
- The Fourth People's Hospital of Wuhu, Wuhu, China
| | - Juan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yong Yang
- Suzhou Guangji Hospital, Affiliated Guangji Hospital of Soochow University, Soochow University, Suzhou, China.
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China; Shanghai Mental Health Center, Shanghai Key Laboratory of Psychiatry Disorders, Shanghai Jiao Tong University, Shanghai, China.
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Li Z, Zhang Q. Ganglioside isomer analysis using ion polarity switching liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 2021; 413:3269-3279. [PMID: 33686479 PMCID: PMC8672327 DOI: 10.1007/s00216-021-03262-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/25/2022]
Abstract
Gangliosides are ubiquitously present on cell surface. They are more abundantly expressed in nerve cells and tissues and involved in pathology of various diseases. Diversity of molecular structures in the carbohydrate head group, fatty acyl, and long chain base increases the complexity of analyzing gangliosides. In this study, an ultrahigh-performance liquid chromatography-tandem mass spectrometry method is developed for analysis of the co-eluting ganglioside isomers, which uses ion polarity switching to integrate glycan head isomer identification, ceramide isomer differentiation, and quantification of ganglioside into one analysis. The method is facilitated with an extensive ganglioside target list by combining the various glycan head groups, long chain bases, and the experimentally determined fatty acyls. Correlation between the retention time of ganglioside and its ceramide total carbon number is experimentally validated and used to predict retention time of ganglioside target list for scheduling the final multiple reaction monitoring method. This method was validated according to the FDA guidelines: 96.5% of gangliosides with good accuracy (80-120%), precision (< 15%), and linearity R2 > 0.99. The authenticated gangliosides were quantified from mouse brain by isotope dilution. Overall, 165 gangliosides were quantified using 10 mg mouse brain tissue, including 100 isomers of GM1, GM2, GM3, GD1a, GD1b, GD2, GD3, and GT1b.
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Affiliation(s)
- Zhucui Li
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA.
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27412, USA.
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Gai QY, Jiao J, Wang X, Fu YJ, Lu Y, Liu J, Wang ZY, Xu XJ. Simultaneous quantification of eleven bioactive phenolic compounds in pigeon pea natural resources and in vitro cultures by ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-QqQ-MS/MS). Food Chem 2021; 335:127602. [PMID: 32739807 DOI: 10.1016/j.foodchem.2020.127602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/18/2020] [Accepted: 07/15/2020] [Indexed: 10/23/2022]
Abstract
Bioactive phenolics primarily contribute to versatile health benefits of pigeon pea. For the first time, an UPLC-QqQ-MS/MS method was developed for the quantitative analysis of eleven bioactive phenolic compounds in pigeon pea natural resources (seeds, leaves, and roots) and in vitro cultures (calli and hairy roots). The proposed method could be achieved within 6 min of running time, and displayed the satisfactory linearity, sensitivity, precision, accuracy, and stability. According to analytical results, the distribution of eleven target compounds in different organs of pigeon pea was clarified. Also, it was surprisingly found that pigeon pea in vitro cultures exhibited superiority in contents of genistin and cajaninstilbene acid as compared with natural resources. Overall, the present work provided a rapid and sensitive analysis approach, which could be useful not only for quality control of pigeon pea natural resources, but also for applicability and safety evaluation of pigeon pea in vitro cultures.
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Affiliation(s)
- Qing-Yan Gai
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China
| | - Jiao Jiao
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China.
| | - Xin Wang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China
| | - Yu-Jie Fu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China.
| | - Yao Lu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China
| | - Jing Liu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China
| | - Zi-Ying Wang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China
| | - Xiao-Jie Xu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, PR China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, PR China
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Fredolini C, Pathak KV, Paris L, Chapple KM, Tsantilas KA, Rosenow M, Tegeler TJ, Garcia-Mansfield K, Tamburro D, Zhou W, Russo P, Massarut S, Facchiano F, Belluco C, De Maria R, Garaci E, Liotta L, Petricoin EF, Pirrotte P. Shotgun proteomics coupled to nanoparticle-based biomarker enrichment reveals a novel panel of extracellular matrix proteins as candidate serum protein biomarkers for early-stage breast cancer detection. Breast Cancer Res 2020; 22:135. [PMID: 33267867 PMCID: PMC7709252 DOI: 10.1186/s13058-020-01373-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background The lack of specificity and high degree of false positive and false negative rates when using mammographic screening for detecting early-stage breast cancer is a critical issue. Blood-based molecular assays that could be used in adjunct with mammography for increased specificity and sensitivity could have profound clinical impact. Our objective was to discover and independently verify a panel of candidate blood-based biomarkers that could identify the earliest stages of breast cancer and complement current mammographic screening approaches. Methods We used affinity hydrogel nanoparticles coupled with LC-MS/MS analysis to enrich and analyze low-abundance proteins in serum samples from 20 patients with invasive ductal carcinoma (IDC) breast cancer and 20 female control individuals with positive mammograms and benign pathology at biopsy. We compared these results to those obtained from five cohorts of individuals diagnosed with cancer in organs other than breast (ovarian, lung, prostate, and colon cancer, as well as melanoma) to establish IDC-specific protein signatures. Twenty-four IDC candidate biomarkers were then verified by multiple reaction monitoring (LC-MRM) in an independent validation cohort of 60 serum samples specifically including earliest-stage breast cancer and benign controls (19 early-stage (T1a) IDC and 41 controls). Results In our discovery set, 56 proteins were increased in the serum samples from IDC patients, and 32 of these proteins were specific to IDC. Verification of a subset of these proteins in an independent cohort of early-stage T1a breast cancer yielded a panel of 4 proteins, ITGA2B (integrin subunit alpha IIb), FLNA (Filamin A), RAP1A (Ras-associated protein-1A), and TLN-1 (Talin-1), which classified breast cancer patients with 100% sensitivity and 85% specificity (AUC of 0.93). Conclusions Using a nanoparticle-based protein enrichment technology, we identified and verified a highly specific and sensitive protein signature indicative of early-stage breast cancer with no false positives when assessing benign and inflammatory controls. These markers have been previously reported in cell-ECM interaction and tumor microenvironment biology. Further studies with larger cohorts are needed to evaluate whether this biomarker panel improves the positive predictive value of mammography for breast cancer detection.
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Affiliation(s)
- Claudia Fredolini
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Khyatiben V Pathak
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Luisa Paris
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Kristina M Chapple
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Kristine A Tsantilas
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Matthew Rosenow
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Tony J Tegeler
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Krystine Garcia-Mansfield
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Davide Tamburro
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Weidong Zhou
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Paul Russo
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Samuele Massarut
- Department of Surgical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081, Aviano, PN, Italy
| | - Francesco Facchiano
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Claudio Belluco
- Department of Surgical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081, Aviano, PN, Italy
| | - Ruggero De Maria
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, 00168, Rome, Italy.,Fondazione Policlinico Universitario "A. Gemelli" - I.R.C.C.S, 00168, Rome, Italy
| | - Enrico Garaci
- University San Raffaele and Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele, Rome, Italy
| | - Lance Liotta
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA.
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Onsurathum S, Kailemia MJ, Intuyod K, Haonon O, Pairojkul C, Thanan R, Pinlaor P, Lebrilla CB, Pinlaor S. N-glycosylation profiling of serum immunoglobulin in opisthorchiasis patients. J Proteomics 2021; 230:103980. [PMID: 32927111 DOI: 10.1016/j.jprot.2020.103980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 11/23/2022]
Abstract
Alteration of immunoglobulin glycosylation correlates with inflammatory diseases and infectious diseases including parasitic infections. Immunoglobulin glycosylation patterns may be implicated in disease development and have also been proposed as diagnostic tools for several diseases. Previous studies have reported the immunoglobulin profiles in experimental animals and in patients infected with the carcinogenic human liver fluke, Opisthorchis viverrini. However, the N-glycosylation profiles of immunoglobulins and their subclass-specific glycoforms in opisthorchiasis patients have never been elucidated. Here, N-glycosylation patterns of immunoglobulins and their subclass-specific glycoforms in sera of O. viverrini-infected patients were investigated using triple quadrupole mass spectrometry coupled with multiple reaction monitoring. Peptide fragmentation was utilized to quantify the immunoglobulin glycoforms normalized to the unique peptide of each subclass. Overall, serum levels of IgG and IgA in O. viverrini patients were significantly increased compared to uninfected controls. Twenty-seven glycoforms were detected based on analysis of detached glycans in all immunoglobulin subclasses. The abundance of immunoglobulin glycopeptides in serum of opisthorchiasis patients deviated significantly from controls. Immunoglobulin glycosylation patterns were associated with both pro- and anti-inflammatory properties. In conclusion, O. viverrini infection alters the serum immunoglobulin glycosylation profile and these changes could distinguish between O. viverrini-infected individuals and healthy controls. SIGNIFICANCE: We demonstrated that both quantities and glycoforms of serum immunoglobulin subclasses were altered in Opisthorchis viverrini-infected individuals as investigated by the QqQ-MS-MRM method. Patterns of immunoglobulin with a specific glycoform might contribute to immune responses to O. viverrini infection.
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40
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An N, Zhu QF, Yu L, Chen YT, Chen SL, Feng YQ. Derivatization assisted LC-p-MRM-MS with high CID voltage for rapid analysis of brassinosteroids. Talanta 2020; 217:121058. [PMID: 32498827 DOI: 10.1016/j.talanta.2020.121058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/11/2020] [Accepted: 04/16/2020] [Indexed: 11/28/2022]
Abstract
In this study, a derivatization-assisted pseudo-multiple reaction monitoring with high CID voltage (HV-p-MRM) strategy was proposed for the analysis of brassinosteroids (BRs) by liquid chromatography-triple quadrupole mass spectrometry (LC-QqQ MS). The concept of the HV-p-MRM strategy was proposed on the basis of an assumption that the precursor ion of analyte is stable in collision cell and less prone to fragmentation at high CID voltage, while co-existing ions (impurity) of easy fragmentation can break down into smaller fragment ions. In such case, by increasing the CID voltage, the co-existing ions that are introduced due to the low resolution of the quadrupole 1 (Q1) can be filtered out by quadrupole 3 (Q3), while the stable precursor ion of analyte will pass through Q3, thereby that the signal-to-noise ratio (S/N) of the analysis can be improved. As a proof-of-concept study, BRs were derivatized with rhodamine B-boronic acid (RhB-BA) and then the derivatives were used to investigate their variations in MS signal, background noise, and S/N upon the CID voltage and MS scanning resolution. The results showed that S/N of these derivatives can be improved in HV-p-MRM mode. To further demonstrate the feasibility of HV-p-MRM strategy, a RhB-BA derivatization assisted LC-HV-p-MRM-MS method was developed for the analysis of BRs. Using this method, rapid and sensitive determination of BRs in different organs of rape flower was achieved. It can be expected that HV-p-MRM may be suitable for the analytes that are stable or can be converted into compounds of high stability in collision cell at high CID voltage.
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Affiliation(s)
- Na An
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Quan-Fei Zhu
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, PR China
| | - Lei Yu
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Yong-Ting Chen
- Hubei Electrochemical Power Sources Key Laboratory, Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Sheng-Li Chen
- Hubei Electrochemical Power Sources Key Laboratory, Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, PR China.
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Hands CM, Sayers RL, Nitride C, Gethings LA, Mills ENC. A multiple reaction monitoring method for determining peanut (Arachis hypogea) allergens in serum using quadrupole and time-of-flight mass spectrometry. Anal Bioanal Chem 2020; 412:2815-2827. [PMID: 32125467 PMCID: PMC7196080 DOI: 10.1007/s00216-020-02508-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/21/2020] [Accepted: 02/11/2020] [Indexed: 11/30/2022]
Abstract
Peanut is a major cause of severe IgE-mediated food allergic reactions, which can be exacerbated by factors, such as exercise, that may increase allergen uptake into the circulation. Enzyme-linked immunosorbent assays (ELISAs) have been used to determine allergen uptake into serum, but there are concerns over their specificity and a confirmatory method is required. Mass spectrometry (MS) methods have the potential to provide rigorous alternatives for allergen determination. A suite of peptide targets representing the major clinically relevant peanut allergens previously applied in food analysis were used to develop a targeted multiple reaction monitoring (MRM) method for determination of peanut in serum. Depletion of serum using affinity chromatography was found to be essential to allow detection of the peptide targets. A comparison of triple quadrupole and Q-TOF methods showed that one Ara h 2 peptide was only detected by the Q-TOF, the other peptide targets giving similar assay sensitivities with both MS platforms, although transitions for all the peptides were detected more consistently with the Q-TOF. The Q-TOF MRM assay detected peanut from spiked serum more effectively than the triple quadrupole assay, with Ara h 3 being detected down to 3 mg total peanut protein/L of serum, comparable with an Ara h 3-specific ELISA. The poor recoveries observed for both methods are likely due to loss of peanut immune complexes during the serum depletion process. Nevertheless, the Q-TOF MRM method has much promise to confirm the uptake of peanut proteins in serum samples providing immune complexes can be disrupted effectively prior to depletion. Graphical abstract.
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Affiliation(s)
- Charlotte M Hands
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Institute of Biotechnology, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M1 7DN, UK
| | - Rebekah L Sayers
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Institute of Biotechnology, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M1 7DN, UK
| | - Chiara Nitride
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Institute of Biotechnology, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M1 7DN, UK
| | - Lee A Gethings
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - E N Clare Mills
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Institute of Biotechnology, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M1 7DN, UK.
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42
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Ziegler J, Hussain H, Neubert RHH, Abel S. Sensitive and Selective Amino Acid Profiling of Minute Tissue Amounts by HPLC/Electrospray Negative Tandem Mass Spectrometry Using 9-Fluorenylmethoxycarbonyl (Fmoc-Cl) Derivatization. Methods Mol Biol 2019; 2030:365-79. [PMID: 31347131 DOI: 10.1007/978-1-4939-9639-1_27] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A method for selective and sensitive quantification of amino acids is described. The combination of established derivatization procedures of secondary and primary amino groups with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) and subsequent detection of derivatized amino acids by LC-ESI-MS/MS using multiple reaction monitoring provides high selectivity. The attachment of an apolar moiety enables purification of derivatized amino acids from matrix by a single solid-phase extraction step, which increases sensitivity by reduced ion suppression during LC-ESI-MS/MS detection. Additionally, chromatography of all amino acids can be performed on reversed-phase HPLC columns using eluents without additives, which are known to cause significant decreases in signal to noise ratios. The method has been routinely applied for amino acid profiling of low amounts of liquids and tissues of various origins with a sample throughput of about 50-100 samples a day. In addition to a detailed description of the method, some representative examples are presented.
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Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair NJT, Hardie DB, Elliott M, Chen L, Newman R, Mohammed Y, Borchers CH. Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation. Mol Cell Proteomics 2020; 19:540-553. [PMID: 31896676 PMCID: PMC7050112 DOI: 10.1074/mcp.tir119.001820] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
The use of protein biomarkers as surrogates for clinical endpoints requires extensive multilevel validation including development of robust and sensitive assays for precise measurement of protein concentration. Multiple reaction monitoring (MRM) is a well-established mass-spectrometric method that can be used for reproducible protein-concentration measurements in biological specimens collected via microsampling. The dried blood spot (DBS) microsampling technique can be performed non-invasively without the expertise of a phlebotomist, and can enhance analyte stability which facilitate the application of this technique in retrospective studies while providing lower storage and shipping costs, because cold-chain logistics can be eliminated. Thus, precise, sensitive, and multiplexed methods for measuring protein concentrations in DBSs can be used for de novo biomarker discovery and for biomarker quantification or verification experiments. To achieve this goal, MRM assays were developed for multiplexed concentration measurement of proteins in DBSs.The lower limit of quantification (LLOQ) was found to have a median total coefficient of variation (CV) of 18% for 245 proteins, whereas the median LLOQ was 5 fmol of peptide injected on column, and the median inter-day CV over 4 days for measuring endogenous protein concentration was 8%. The majority (88%) of the assays displayed parallelism, whereas the peptide standards remained stable throughout the assay workflow and after exposure to multiple freeze-thaw cycles. For 190 proteins, the measured protein concentrations remained stable in DBS stored at ambient laboratory temperature for up to 2 months. Finally, the developed assays were used to measure the concentration ranges for 200 proteins in twenty same sex, same race and age matched individuals.
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Affiliation(s)
- Azad Eshghi
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada.
| | - Adam J Pistawka
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Michael Chen
- Island Medical Program, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Nicholas J T Sinclair
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Monica Elliott
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Lei Chen
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Rachael Newman
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Yassene Mohammed
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada; Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christoph H Borchers
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Department of Data Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Nobel St., Moscow143026, Russia.
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44
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Li Z, Zhang X, Liao J, Fan X, Cheng Y. An ultra-robust fingerprinting method for quality assessment of traditional Chinese medicine using multiple reaction monitoring mass spectrometry. J Pharm Anal 2020; 11:88-95. [PMID: 33717615 PMCID: PMC7930630 DOI: 10.1016/j.jpha.2020.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/28/2019] [Accepted: 01/13/2020] [Indexed: 11/30/2022] Open
Abstract
Chromatographic fingerprinting has been perceived as an essential tool for assessing quality and chemical equivalence of traditional Chinese medicine. However, this pattern-oriented approach still has some weak points in terms of chemical coverage and robustness. In this work, we proposed a multiple reaction monitoring (MRM)-based fingerprinting method in which approximately 100 constituents were simultaneously detected for quality assessment. The derivative MRM approach was employed to rapidly design MRM transitions independent of chemical standards, based on which the large-scale fingerprinting method was efficiently established. This approach was exemplified on QiShenYiQi Pill (QSYQ), a traditional Chinese medicine-derived drug product, and its robustness was systematically evaluated by four indices: clustering analysis by principal component analysis, similarity analysis by the congruence coefficient, the number of separated peaks, and the peak area proportion of separated peaks. Compared with conventional ultraviolet-based fingerprints, the MRM fingerprints provided not only better discriminatory capacity for the tested normal/abnormal QSYQ samples, but also higher robustness under different chromatographic conditions (i.e., flow rate, apparent pH, column temperature, and column). The result also showed for such large-scale fingerprints including a large number of peaks, the angle cosine measure after min-max normalization was more suitable for setting a decision criterion than the unnormalized algorithm. This proof-of-concept application gives evidence that combining MRM technique with proper similarity analysis metrices can provide a highly sensitive, robust and comprehensive analytical approach for quality assessment of traditional Chinese medicine. MRM fingerprints are proposed for quality assessment of traditional medicine. MRM fingerprints show favorable robustness, coverage and discriminatory capacity. Similarity analysis methods for such large-scale fingerprints are proposed.
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Affiliation(s)
- Zhenhao Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohui Zhang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiyu Cheng
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
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45
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Abstract
Recently, the sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) method coupled with liquid chromatography has been demonstrated for the quantification of isotopic 13C enrichment in a large number of cellular metabolites and fragments. SWATH, a data-independent acquisition (DIA) method, alleviates the need for data deconvolution and shows greater accuracy in the quantification of low abundance isotopologs of fragments thereby resulting in a lower systematic error. Here we provide a detailed protocol for the design of Q1 mass isolation windows and the post-acquisition data analysis with emphasis on the untargeted nature of SWATH.
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Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India.
- DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Mumbai, India.
- Wadhwani Research Centre for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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46
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Oeckl P, Weydt P, Thal DR, Weishaupt JH, Ludolph AC, Otto M. Proteomics in cerebrospinal fluid and spinal cord suggests UCHL1, MAP2 and GPNMB as biomarkers and underpins importance of transcriptional pathways in amyotrophic lateral sclerosis. Acta Neuropathol 2020; 139:119-134. [PMID: 31701227 DOI: 10.1007/s00401-019-02093-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/11/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease and the proteins and pathways involved in the pathophysiology are not fully understood. Even less is known about the preclinical disease phase. To uncover new ALS-related proteins and pathways, we performed a comparative proteomic analysis in cerebrospinal fluid (CSF) of asymptomatic (n = 14) and symptomatic (n = 14) ALS mutation carriers and sporadic ALS patients (n = 12) as well as post-mortem human spinal cord tissue (controls: n = 7, ALS, n = 8). Using a CSF-optimized proteomic workflow, we identified novel (e.g., UCHL1, MAP2, CAPG, GPNMB, HIST1H4A, HIST1H2B) and well-described (e.g., NEFL, NEFH, NEFM, CHIT1, CHI3L1) protein level changes in CSF of sporadic and genetic ALS patients with enrichment of proteins related to transcription, cell cycle and lipoprotein remodeling (total protein IDs: 2303). No significant alteration was observed in asymptomatic ALS mutation carriers representing the prodromal disease phase. We confirmed UCHL1, MAP2, CAPG and GPNMB as novel biomarker candidates for ALS in an independent validation cohort of patients (n = 117) using multiple reaction monitoring. In spinal cord tissue, 292 out of 6810 identified proteins were significantly changed in ALS with enrichment of proteins involved in mRNA splicing and of the neurofilament compartment. In conclusion, our proteomic data in asymptomatic ALS mutation carriers support the hypothesis of a sudden disease onset instead of a long preclinical phase. Both CSF and tissue proteomic data indicate transcriptional pathways to be amongst the most affected. UCHL1, MAP2 and GPNMB are promising ALS biomarker candidates which might provide additional value to the established neurofilaments in patient follow-up and clinical trials.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Patrick Weydt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Dietmar R Thal
- Laboratory of Neuropathology, Institute of Pathology, Ulm University, Ulm, Germany
- Department of Imaging and Pathology, KU Leuven and Department of Pathology, UZ Leuven, Louvain, Belgium
| | - Jochen H Weishaupt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Albert C Ludolph
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany.
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47
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Abstract
The apolipoproteins are well known for their roles in both health and disease, as components of plasma lipoprotein particles, such as high-density lipoprotein (HDL), low-density lipoprotein (LDL), very-low-density lipoprotein (VLDL), chylomicrons, and metabolic, vascular- and inflammation-related disorders, such as cardiovascular disease, atherosclerosis, metabolic syndrome, and diabetes. Increasingly, their roles in neurovascular and neurodegenerative disorders are also being elucidated. They play major roles in lipid and cholesterol transport between blood and organs and are, therefore, critical to maintenance and homeostasis of the lipidome, with apolipoprotein-lipid interactions, including cholesterol, fatty acids, triglycerides, phospholipids, and isoprostanes. Further, they have important pleiotropic roles related to aging and longevity, which are largely managed through their many structural variants, including multiple isoforms, and a diversity of post-translational modifications. Consequently, tools for the characterization and accurate quantification of apolipoproteins, including their diverse array of variant forms, are required to understand their salutary and disease related roles. In this chapter we outline three distinct quantitative approaches suitable for targeting apolipoproteins: (1) multiplex immunoassays, (2) mass spectrometric immunoassay, and (3) multiple reaction monitoring, mass spectrometric quantification. We also discuss management of pre-analytical and experimental design variables.
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48
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López-Bascón MA, Calderón-Santiago M, Díaz-Lozano A, Camargo A, López-Miranda J, Priego-Capote F. Development of a qualitative/quantitative strategy for comprehensive determination of polar lipids by LC-MS/MS in human plasma. Anal Bioanal Chem 2019; 412:489-498. [PMID: 31760450 DOI: 10.1007/s00216-019-02261-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/22/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022]
Abstract
Polar lipids, especially glycerophospholipids, constitute the main components of cell membranes and are precursors of signaling molecules in many cellular and physiological processes. For this reason, the development of methods with high capability for detection of polar lipids in biological samples is required. In this research, the objective was to develop a method for comprehensive qualitative/quantitative determination of polar lipids in plasma by a combination of acquisition methods with a triple quadrupole mass analyzer. The strategy was optimized in two steps: (a) a first step for detection of lipids by monitoring selective fragmentation patterns representative of each lipid family and (b) a second step for confirmation of lipid species by detection and identification of product ions associated with the conjugated fatty acids. The acquisition list was divided into two multiple reaction monitoring (MRM) methods to ensure the detection of all transitions with suited instrumental sensitivity according to chromatographic retention time and relative abundance in plasma. The combination of the two MRM methods allowed the detection of 398 polar lipids in plasma in 64 min. Precision, estimated as within-day variability, was below 6.8% for all determined lipid families, while between-day variability was below 24.0%. This strategy has been applied to a cohort formed by 384 individuals in order to obtain a qualitative and quantitative distribution of polar lipids in human plasma. The most concentrated lipid families in relative terms were lysophospholipids, plasmalogens, and phosphatydilcholines, with mean relative concentration of 58.0, 17.1, and 8.3%, respectively. Then, sphingomyelins and phosphatidylethanolamines reported a relative concentration of 2.0%, followed by phosphatidylserines, with 1.1%. Graphical abstract.
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Affiliation(s)
- M A López-Bascón
- Department of Analytical Chemistry, University of Córdoba, 14071, Córdoba, Spain.,Maimónides Institute for Biomedical Research (IMIBIC)/University of Córdoba/Reina Sofía University Hospital, 14004, Córdoba, Spain.,CeiA3 Agroalimentary Excellence Campus, University of Córdoba, 14071, Córdoba, Spain.,CIBER Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - M Calderón-Santiago
- Department of Analytical Chemistry, University of Córdoba, 14071, Córdoba, Spain. .,Maimónides Institute for Biomedical Research (IMIBIC)/University of Córdoba/Reina Sofía University Hospital, 14004, Córdoba, Spain. .,CeiA3 Agroalimentary Excellence Campus, University of Córdoba, 14071, Córdoba, Spain. .,CIBER Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Salud Carlos III, 28220, Madrid, Spain.
| | - A Díaz-Lozano
- Department of Analytical Chemistry, University of Córdoba, 14071, Córdoba, Spain.,Maimónides Institute for Biomedical Research (IMIBIC)/University of Córdoba/Reina Sofía University Hospital, 14004, Córdoba, Spain.,CeiA3 Agroalimentary Excellence Campus, University of Córdoba, 14071, Córdoba, Spain.,CIBER Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - A Camargo
- Maimónides Institute for Biomedical Research (IMIBIC)/University of Córdoba/Reina Sofía University Hospital, 14004, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - J López-Miranda
- Maimónides Institute for Biomedical Research (IMIBIC)/University of Córdoba/Reina Sofía University Hospital, 14004, Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - F Priego-Capote
- Department of Analytical Chemistry, University of Córdoba, 14071, Córdoba, Spain. .,Maimónides Institute for Biomedical Research (IMIBIC)/University of Córdoba/Reina Sofía University Hospital, 14004, Córdoba, Spain. .,CeiA3 Agroalimentary Excellence Campus, University of Córdoba, 14071, Córdoba, Spain. .,CIBER Fragilidad y Envejecimiento Saludable (CIBERfes), Instituto de Salud Carlos III, 28220, Madrid, Spain.
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Chu HW, Chang KP, Hsu CW, Chang IYF, Liu HP, Chen YT, Wu CC. Identification of Salivary Biomarkers for Oral Cancer Detection with Untargeted and Targeted Quantitative Proteomics Approaches. Mol Cell Proteomics 2019; 18:1796-1806. [PMID: 31253657 PMCID: PMC6731081 DOI: 10.1074/mcp.ra119.001530] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 01/08/2023] Open
Abstract
Oral cavity squamous cell carcinoma (OSCC) is one of the most common cancers worldwide. In Taiwan, OSCC is the fifth leading cause of cancer-related mortality and leads to 2800 deaths per year. The poor outcome of OSCC patients is principally ascribed to the fact that this disease is often advanced at the time of diagnosis, suggesting that early detection of OSCC is urgently needed. Analysis of cancer-related body fluids is one promising approach to identify biomarker candidates of cancers. To identify OSCC biomarkers, salivary proteomes of OSCC patients, individuals with oral potentially malignant disorders (OPMDs), and healthy volunteers were comparatively profiled with isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry (MS). The salivary levels of 67 and 18 proteins in the OSCC group are elevated and decreased compared with that in the noncancerous group (OPMD and healthy groups), respectively. The candidate biomarkers were further selected using the multiple reaction monitoring (MRM)-MS and validated with the immunoassays. More importantly, the higher salivary level of three proteins, complement factor H (CFH), fibrinogen alpha chain (FGA), and alpha-1-antitrypsin (SERPINA1) was correlated with advanced stages of OSCC. Our results indicate that analysis of salivary proteome is a feasible strategy for biomarker discovery, and the three proteins are potential salivary markers for OSCC diagnosis.
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Affiliation(s)
- Hao-Wei Chu
- ‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kai-Ping Chang
- §Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Chia-Wei Hsu
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hao-Ping Liu
- ‖Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ting Chen
- ‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; **Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; ‡‡Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Chih-Ching Wu
- ‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; §Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; §§Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan; ¶¶Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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50
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Wang T, Nguyen A, Zhang L, Turko IV. Mass spectrometry enumeration of filamentous M13 bacteriophage. Anal Biochem 2019; 582:113354. [PMID: 31276652 DOI: 10.1016/j.ab.2019.113354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/11/2019] [Accepted: 06/29/2019] [Indexed: 11/18/2022]
Abstract
In the last decade, filamentous M13 bacteriophage has emerged into numerous biotechnological applications as a promising nontoxic and self-assembling biomaterial with specific binding properties. This raises a question about its upscale production that consequently requires an accurate phage enumeration during the various protocol developments. However, traditional methods of measuring phage concentration are mainly biological in nature and therefore time and labor intensive. These traditional methods also demonstrate poor reproducibility and are semi-quantitative at best. In the present work, we capitalized on mass spectrometry based absolute protein quantitation. We have optimized the quantitation conditions for a major coat protein, pVIII. Enumeration of M13 bacteriophage can be further performed using the determined molar concentration of pVIII, Avogadro's number, and known copy number of pVIII per phage. Since many different phages have well-defined copy number of capsid proteins, the proposed approach can be simply applied to any phage with known copy number of a specific capsid protein.
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Affiliation(s)
- Tingting Wang
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States; Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, United States; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32601, United States
| | - Ai Nguyen
- Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, United States
| | - Linwen Zhang
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States; Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, United States
| | - Illarion V Turko
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States; Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, United States.
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