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Arena S, Renzone G, Ciaravolo V, Scaloni A. Albumen and Yolk Plasma Peptidomics for the Identification and Quantitation of Bioactive Molecules and the Quality Control of Hen Egg Products. Methods Mol Biol 2024; 2758:241-254. [PMID: 38549018 DOI: 10.1007/978-1-0716-3646-6_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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Hen eggs and the corresponding food products are essential components of human diet. In addition to supplying basic nutrients, they contain functional peptides that are released in vivo within the intact raw material following physiological proteolytic events affecting specific proteins or derive from technological processing of albumen and yolk fractions as a result of the dedicated use of proteases from plant and microbial sources. Besides their potential importance for functional applications, peptides released under physiological conditions in intact egg can be used as markers of product storage and deterioration. Therefore, characterization and quantitation of peptides in egg and egg-derived products can be used to implement evaluation of potential bioactivities as well as to assess food product qualitative characteristics. Here, we provide dedicated information on extraction, identification, and quantitative analysis of peptides from albumen and yolk plasma; nano-liquid chromatography-mass spectrometry combined with bioinformatic analysis of resulting raw data by different software tools allowed to assign molecules based on database searching and to evaluate their relative quantity in different samples.
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Affiliation(s)
- Simona Arena
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici, Italy
| | - Giovanni Renzone
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici, Italy
| | - Valentina Ciaravolo
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici, Italy
| | - Andrea Scaloni
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici, Italy.
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Kress J, Nandita E, Jones E, Sanou M, Higgins J, Kosanam H. A targeted liquid chromatography mass spectrometry method for routine monitoring of cell culture media components for bioprocess development. J Chromatogr A 2023; 1706:464281. [PMID: 37566999 DOI: 10.1016/j.chroma.2023.464281] [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: 02/18/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
The analysis of cell culture media (CCM) components is critical for understanding cell growth kinetics and overall product quality during biomanufacturing. Given the diverse physical and chemical nature of CCM compounds present at a wide range of concentrations, there is an increasing demand for single-platform analytical assays with exceptional specificity and sensitivity. This study presents a targeted LC-MS/MS method for the identification and quantitation of 110 CCM analytes is presented, where target metabolites are monitored over an 20-min gradient. The analyte panel constitutes amino acids, vitamins, organic acids, nucleic acids, carbohydrates, and lipids. The method employs isotopically labeled standards to enable specific and accurate relative quantitation of CCM compounds based on physicochemical properties and retention time. Quantitation is performed on a triple quadrupole mass spectrometer operated in multiple reaction monitoring (MRM) mode. The method demonstrates strong linearity with an R2 of ≥0.99 with three orders of linear dynamic range and inter-day and intra-day precision with a%CV of <10% for spiked-in quality control samples. We also present three case studies to demonstrate method applicability in the bioprocessing space for developing vaccines and biologics.
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Affiliation(s)
- Jared Kress
- Global Vaccines and Biologics Commercialization, Merck & Co., Inc, West Point, PA, USA
| | | | | | - Missa Sanou
- Global Vaccines and Biologics Commercialization, Merck & Co., Inc, West Point, PA, USA
| | - John Higgins
- Global Vaccines and Biologics Commercialization, Merck & Co., Inc, West Point, PA, USA
| | - Hari Kosanam
- Global Vaccines and Biologics Commercialization, Merck & Co., Inc, West Point, PA, USA.
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Wen SS, Zhou HS, Zhu CS, Li P, Gao W. Direct infusion electrospray ionization-ion mobility-mass spectrometry for rapid metabolite marker discovery of medicinal Phellodendron Bark. J Pharm Biomed Anal 2022; 219:114939. [PMID: 35908412 DOI: 10.1016/j.jpba.2022.114939] [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: 04/27/2022] [Revised: 07/02/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022]
Abstract
Ion-mobility mass spectrometry (IM-MS) currently serves as a powerful tool for the structural identification of numerous biological compounds and small molecules. In this work, rapid metabolomic analysis of closely-related herbal medicines by direct injection ion mobility-quadrupole time-of-flight mass spectrometry (DI-IM-QTOF MS) was established. Phellodendron chinense Bark (PC) and Phellodendron amurense Bark (PA) were studied as a case. Thirty-three batches of PC and twenty-two batches of PA have been directly injected in electrospray ionization-IM-QTOF MS in positive mode. Without chromatographic separation, each run was completed within 3 min. After data alignment and statistical analysis, a total of seven chemical markers were found (p-value < 0.05, VIP > 1.00). Among them, the ion m/z 342.17 and m/z 356.18 present a single peak in the drift spectrum, respectively, but their drift time has a certain deviation compared with the pure substance of known compounds. In addition, the MS/MS spectra also confirmed that the single peak includes two chemical isomers. To investigate the composition ratio of individual isomers, the calibration curves of relative drift time (rDT) based on the standard superposition method were established, which were found to fit the least square regression. The ion [M]+m/z 342.17 was recognized consisting of magnoflorine (MAG) and phellodendrine (PHE), and their composition ratio in PA and PC samples was calculated. The results were compared with those obtained by the HPLC quantitative method, which produced equivalent quantification results. Our DI-IM-QTOF MS methodology provides an additional methodology for the relative quantification of unresolved isomers in drift tube IM-MS and offers DI-IM-QTOF MS based metabolomics.
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Affiliation(s)
- Shan-Shan Wen
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Hong-Shan Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Chuan-Sheng Zhu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China.
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Minchev DS, Popov NT, Naimov SI, Minkov IN, Vachev TI. Comparative Expression Analysis of Human Endogenous Retrovirus Elements in Peripheral Blood of Children with Specific Language Impairment. Balkan J Med Genet 2019; 22:49-56. [PMID: 31523620 DOI: 10.2478/bjmg-2019-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Specific language impairment (SLI) is a psychiatric condition with a complex etiology and a substantial genetic basis that affects children's verbal communication abilities. In this study, we examined the expression of five different human endogenous retrovirus elements (HERVs) in a cohort of 25 children with SLI and 25 healthy children in the control group. Human endogenous retrovirus elements, a diverse group of repetitive DNA sequences, can potentially cause considerable genetic heterogeneity. They had been integrated in the genome of our ancestors throughout evolution and now consist of about 8.0% of the human genome. Several HERV loci are transcribed in various cell types. Their expression in peripheral blood and in the brain is altered in many neurological and psychiatric diseases. To date, HERV expression profiles have never been studied in patients with SLI. This study aimed to elucidate differentially regulated human endogenous retroelements in peripheral blood of children with SLI, in comparison with healthy controls, through quantitative reverse tran-scription-polymerase chain reaction (qRT-PCR) methodology. Our results show that two genes: HERV-K (HLM-2) gag and HERV-P env were expressed at lower levels in the blood samples from SLI children in comparison with those in the control group.
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Lahiri P, Dhaware D, Singh A, Panchagnula V, Ghosh D. Quantitation of Neurotoxic Metabolites of the Kynurenine Pathway by Laser Desorption Ionization Mass Spectrometry (LDI-MS). Methods Mol Biol 2019; 1996:113-129. [PMID: 31127552 DOI: 10.1007/978-1-4939-9488-5_11] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The metabolites of the mammalian kynurenine (KYN) pathway are generated from a branch of tryptophan metabolic pathway. The latter generates 3-hydroxykynurenine (3-HK), kynurenic acid (KYNA), quinolinic acid (QUIN), and picolinic acid (PIC) which are all strongly neuroactive, often with dramatically contrasting functional outcomes. Whereas KYNA and PIC are neuroprotective, 3-HK and QUIN are potently neurotoxic and attributed in major neurodegenerative diseases like schizophrenia, Alzheimer's disease, Huntington's disease, bipolar disorder, and depression. It is increasingly evident that the ratio(s) between the neurotoxic and neuroprotective metabolites may help predict the manifestations of disease vs. health. Therefore high-throughput platforms for determining the relative levels of these kynurenine metabolites in biofluids offer considerable potential. Current analytical tools for studying KYN pathway include assays of branching enzymes, PCR, immunoanalysis, and LCMS. None of these offer high-throughput, cost-effective analyses suited for clinical or drug-screening applications. In this report a laser desorption ionization mass spectrometry (LDI-MS) method is described using SBA-15 mesoporous silica. The system allows fast, high-resolution quantitation of neurotoxic kynurenines using targeted metabolomics on conventional MALDI platforms.
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Affiliation(s)
- Pallavi Lahiri
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Deepika Dhaware
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, India
| | - Ajeet Singh
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, India
| | - Venkateswarlu Panchagnula
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, India
| | - Dipankar Ghosh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
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Trzeciecka A, Pattabiraman P, Piqueras MC, Toris C, Bhattacharya SK. Quantitative Proteomic Analysis of Human Aqueous Humor Using iTRAQ 4plex Labeling. Methods Mol Biol 2018; 1695:89-95. [PMID: 29190021 DOI: 10.1007/978-1-4939-7407-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
iTRAQ 4plex method enables multiplexing of up to four samples for simultaneous quantitation to improve sensitivity and scope of proteomic analysis. Here, we describe iTRAQ 4plex labeling of human aqueous humor specimens followed by ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and data analysis for peptide identification and quantitation using Proteome Discoverer software. The protocol can be applied for other animals as well; however, pooling of specimens may be required to obtain sufficient amount of protein for labeling.
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Tuomivaara ST, Schliekelman P, Nairn AV, Moremen KW, York WS. RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM). Anal Chim Acta 2017; 993:22-37. [PMID: 29078952 DOI: 10.1016/j.aca.2017.09.023] [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: 03/02/2017] [Revised: 07/27/2017] [Accepted: 09/12/2017] [Indexed: 10/18/2022]
Abstract
Motivated by the lack of easily implementable and generally applicable strategies to increase and assess data accuracy, we devised a novel label-free approach, termed REQUIEM, to address challenges in relative quantitation. For comparing the relative amounts of analytes in two samples, a mixture is prepared from aliquots of the samples, and the samples and the mixture are analyzed in parallel according to the intended workflow. Processing of the resulting data using the REQUIEM algorithm yields unbiased analyte fold-changes and associated statistics, allowing several types of errors to be diagnosed or eliminated. Extensive simulations and analysis of carefully prepared standard samples demonstrated the rigorous foundations of REQUIEM. We applied REQUIEM to several real-world analytical techniques and workflows, notably to tandem mass spectrometry analysis by using isomeric oligosaccharides as test analytes. We conclude that REQUIEM can reveal inaccuracies in the data that are difficult to identify by using traditional approaches.
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Affiliation(s)
- Sami T Tuomivaara
- Complex Carbohydrate Research Center, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Paul Schliekelman
- The Department of Statistics, 101 Cedar St, University of Georgia, Athens, GA 30602, USA
| | - Alison V Nairn
- Complex Carbohydrate Research Center, 315 Riverbend Rd, Athens, GA 30602, USA; The Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, 315 Riverbend Rd, Athens, GA 30602, USA; The Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - William S York
- Complex Carbohydrate Research Center, 315 Riverbend Rd, Athens, GA 30602, USA; The Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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Dator R, Carrà A, Maertens L, Guidolin V, Villalta PW, Balbo S. A High Resolution/Accurate Mass (HRAM) Data-Dependent MS 3 Neutral Loss Screening, Classification, and Relative Quantitation Methodology for Carbonyl Compounds in Saliva. J Am Soc Mass Spectrom 2017; 28:608-618. [PMID: 27785693 PMCID: PMC5772964 DOI: 10.1007/s13361-016-1521-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 07/29/2016] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 06/06/2023]
Abstract
Reactive carbonyl compounds (RCCs) are ubiquitous in the environment and are generated endogenously as a result of various physiological and pathological processes. These compounds can react with biological molecules inducing deleterious processes believed to be at the basis of their toxic effects. Several of these compounds are implicated in neurotoxic processes, aging disorders, and cancer. Therefore, a method characterizing exposures to these chemicals will provide insights into how they may influence overall health and contribute to disease pathogenesis. Here, we have developed a high resolution accurate mass (HRAM) screening strategy allowing simultaneous identification and relative quantitation of DNPH-derivatized carbonyls in human biological fluids. The screening strategy involves the diagnostic neutral loss of hydroxyl radical triggering MS3 fragmentation, which is only observed in positive ionization mode of DNPH-derivatized carbonyls. Unique fragmentation pathways were used to develop a classification scheme for characterizing known and unanticipated/unknown carbonyl compounds present in saliva. Furthermore, a relative quantitation strategy was implemented to assess variations in the levels of carbonyl compounds before and after exposure using deuterated d 3 -DNPH. This relative quantitation method was tested on human samples before and after exposure to specific amounts of alcohol. The nano-electrospray ionization (nano-ESI) in positive mode afforded excellent sensitivity with detection limits on-column in the high-attomole levels. To the best of our knowledge, this is the first report of a method using HRAM neutral loss screening of carbonyl compounds. In addition, the method allows simultaneous characterization and relative quantitation of DNPH-derivatized compounds using nano-ESI in positive mode. Graphical Abstract ᅟ.
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Affiliation(s)
- Romel Dator
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Andrea Carrà
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Laura Maertens
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Valeria Guidolin
- Department of Analytical Chemistry, University of Turin, Via Pietro Giuria 5, 10125, Turin, Italy
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA.
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Amoroso MG, Galiero G, Fusco G. Genetic characterization of ovine herpesvirus 2 strains involved in water buffaloes malignant catarrhal fever outbreaks in Southern Italy. Vet Microbiol 2016; 199:31-35. [PMID: 28110782 DOI: 10.1016/j.vetmic.2016.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 10/07/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
Abstract
Ovine herpesvirus 2 (OvHV-2) was responsible for two outbreaks of malignant catarrhal fever (MCF) on two water buffalo farms in Southern Italy. In this study, the presence of this virus in the nasal swabs from sick animals as well as in the organs of dead buffaloes was ascertained by a Real-time PCR assay. Positive samples also underwent a relative quantitative analysis of the viral DNA in them. All the dead animals had the highest relative viral quantities, while buffaloes recovering from the virus had intermediate quantities, and asymptomatic OvHV-2-positive sheep had the lowest relative quantities (as compared with the calibrator). The strains involved in the MCF outbreaks underwent genetic characterization by sequencing segments of their ORF50, ORF75 and Ov9.5 genes. The results showed that the outbreaks were caused by two specific genetic variants of OvHV-2, and that these variants exhibit nucleotide differences at the loci analysed. Sheep living in the surrounding farms, as well as sheep kept with buffaloes, were also investigated as possible transmitters of the virus. In this regard, local strategies for the control of MCF should consider separating reservoir species from susceptible animals.
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Affiliation(s)
- Maria Grazia Amoroso
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute, 2, 80055 Portici (NA), Italy.
| | - Giorgio Galiero
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute, 2, 80055 Portici (NA), Italy
| | - Giovanna Fusco
- Department of Animal Health, Experimental Zooprophylactic Institute of Southern Italy, Via Salute, 2, 80055 Portici (NA), Italy.
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Mawuenyega KG, Kasten T, Sigurdson W, Bateman RJ. Amyloid-beta isoform metabolism quantitation by stable isotope-labeled kinetics. Anal Biochem 2013; 440:56-62. [PMID: 23714261 DOI: 10.1016/j.ab.2013.04.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 11/22/2022]
Abstract
Abundant evidence suggests a central role for the amyloid-beta (Aβ) peptide in Alzheimer's disease (AD) pathogenesis. Production and clearance of different Aβ isoforms have been established as targets of proposed disease-modifying therapeutic treatments of AD. However, previous studies used multiple sequential purification steps to isolate the isoforms individually and quantitate them based on a common mid-domain peptide. We created a method to simultaneously purify Aβ isoforms and quantitate them by the specific C-terminal peptides in order to investigate Aβ isoform physiology in the central nervous system. By using standards generated from in vitro metabolic labeling, the relative quantitation of four peptides representing total amount of Aβ (Aβ-Total), Aβ38, Aβ40, and Aβ42 were achieved both in cell culture and in human cerebrospinal fluid (CSF). Standard curves for each isoform demonstrated good sensitivity with very low limits of detection and high accuracy. Because the assay does not require antibody development for each Aβ isoform peptide, significant improvements in the throughput and accuracy of isoform quantitation were achieved.
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