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Sarkar S, Roy D, Chatterjee B, Ghosh R. Clinical advances in analytical profiling of signature lipids: implications for severe non-communicable and neurodegenerative diseases. Metabolomics 2024; 20:37. [PMID: 38459207 DOI: 10.1007/s11306-024-02100-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Lipids play key roles in numerous biological processes, including energy storage, cell membrane structure, signaling, immune responses, and homeostasis, making lipidomics a vital branch of metabolomics that analyzes and characterizes a wide range of lipid classes. Addressing the complex etiology, age-related risk, progression, inflammation, and research overlap in conditions like Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and Cancer poses significant challenges in the quest for effective therapeutic targets, improved diagnostic markers, and advanced treatments. Mass spectrometry is an indispensable tool in clinical lipidomics, delivering quantitative and structural lipid data, and its integration with technologies like Liquid Chromatography (LC), Magnetic Resonance Imaging (MRI), and few emerging Matrix-Assisted Laser Desorption Ionization- Imaging Mass Spectrometry (MALDI-IMS) along with its incorporation into Tissue Microarray (TMA) represents current advances. These innovations enhance lipidomics assessment, bolster accuracy, and offer insights into lipid subcellular localization, dynamics, and functional roles in disease contexts. AIM OF THE REVIEW The review article summarizes recent advancements in lipidomic methodologies from 2019 to 2023 for diagnosing major neurodegenerative diseases, Alzheimer's and Parkinson's, serious non-communicable cardiovascular diseases and cancer, emphasizing the role of lipid level variations, and highlighting the potential of lipidomics data integration with genomics and proteomics to improve disease understanding and innovative prognostic, diagnostic and therapeutic strategies. KEY SCIENTIFIC CONCEPTS OF REVIEW Clinical lipidomic studies are a promising approach to track and analyze lipid profiles, revealing their crucial roles in various diseases. This lipid-focused research provides insights into disease mechanisms, biomarker identification, and potential therapeutic targets, advancing our understanding and management of conditions such as Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and specific cancers.
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Affiliation(s)
- Sutanu Sarkar
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Deotima Roy
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Bhaskar Chatterjee
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Rajgourab Ghosh
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India.
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2
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Lee MJ, Cho JY, Bae S, Jung HS, Kang CM, Kim SH, Choi HJ, Lee CK, Kim H, Jo D, Paik YK. Inhibition of the Alternative Complement Pathway May Cause Secretion of Factor B, Enabling an Early Detection of Pancreatic Cancer. J Proteome Res 2024; 23:985-998. [PMID: 38306169 DOI: 10.1021/acs.jproteome.3c00695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
This study aims to elucidate the cellular mechanisms behind the secretion of complement factor B (CFB), known for its dual roles as an early biomarker for pancreatic ductal adenocarcinoma (PDAC) and as the initial substrate for the alternative complement pathway (ACP). Using parallel reaction monitoring analysis, we confirmed a consistent ∼2-fold increase in CFB expression in PDAC patients compared with that in both healthy donors (HD) and chronic pancreatitis (CP) patients. Elevated ACP activity was observed in CP and other benign conditions compared with that in HD and PDAC patients, suggesting a functional link between ACP and PDAC. Protein-protein interaction analyses involving key complement proteins and their regulatory factors were conducted using blood samples from PDAC patients and cultured cell lines. Our findings revealed a complex control system governing the ACP and its regulatory factors, including Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation, adrenomedullin (AM), and complement factor H (CFH). Particularly, AM emerged as a crucial player in CFB secretion, activating CFH and promoting its predominant binding to C3b over CFB. Mechanistically, our data suggest that the KRAS mutation stimulates AM expression, enhancing CFH activity in the fluid phase through binding. This heightened AM-CFH interaction conferred greater affinity for C3b over CFB, potentially suppressing the ACP cascade. This sequence of events likely culminated in the preferential release of ductal CFB into plasma during the early stages of PDAC. (Data set ID PXD047043.).
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Affiliation(s)
- Min Jung Lee
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
| | - Jin-Young Cho
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
| | - Sumi Bae
- JW BioScience Corp., 38 Gwacheon-daero, Gwacheon-si, Gyeonggi-do 13840, South Korea
| | - Hye Soo Jung
- JW BioScience Corp., 38 Gwacheon-daero, Gwacheon-si, Gyeonggi-do 13840, South Korea
| | - Chang Moo Kang
- Department of Surgery, Division of HBP Surgery, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sung Hyun Kim
- Department of Surgery, Division of HBP Surgery, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Hye Jin Choi
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Choong-Kun Lee
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Daewoong Jo
- Cellivery R&D Institute, Cellivery Therapeutics, Inc., Seoul 03929, Korea
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
- Cellivery R&D Institute, Cellivery Therapeutics, Inc., Seoul 03929, Korea
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3
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Ryu J, Boylan KLM, Twigg CAI, Evans R, Skubitz APN, Thomas SN. Quantification of putative ovarian cancer serum protein biomarkers using a multiplexed targeted mass spectrometry assay. Clin Proteomics 2024; 21:1. [PMID: 38172678 PMCID: PMC10762856 DOI: 10.1186/s12014-023-09447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Ovarian cancer is the most lethal gynecologic malignancy in women, and high-grade serous ovarian cancer (HGSOC) is the most common subtype. Currently, no clinical test has been approved by the FDA to screen the general population for ovarian cancer. This underscores the critical need for the development of a robust methodology combined with novel technology to detect diagnostic biomarkers for HGSOC in the sera of women. Targeted mass spectrometry (MS) can be used to identify and quantify specific peptides/proteins in complex biological samples with high accuracy, sensitivity, and reproducibility. In this study, we sought to develop and conduct analytical validation of a multiplexed Tier 2 targeted MS parallel reaction monitoring (PRM) assay for the relative quantification of 23 putative ovarian cancer protein biomarkers in sera. METHODS To develop a PRM method for our target peptides in sera, we followed nationally recognized consensus guidelines for validating fit-for-purpose Tier 2 targeted MS assays. The endogenous target peptide concentrations were calculated using the calibration curves in serum for each target peptide. Receiver operating characteristic (ROC) curves were analyzed to evaluate the diagnostic performance of the biomarker candidates. RESULTS We describe an effort to develop and analytically validate a multiplexed Tier 2 targeted PRM MS assay to quantify candidate ovarian cancer protein biomarkers in sera. Among the 64 peptides corresponding to 23 proteins in our PRM assay, 24 peptides corresponding to 16 proteins passed the assay validation acceptability criteria. A total of 6 of these peptides from insulin-like growth factor-binding protein 2 (IBP2), sex hormone-binding globulin (SHBG), and TIMP metalloproteinase inhibitor 1 (TIMP1) were quantified in sera from a cohort of 69 patients with early-stage HGSOC, late-stage HGSOC, benign ovarian conditions, and healthy (non-cancer) controls. Confirming the results from previously published studies using orthogonal analytical approaches, IBP2 was identified as a diagnostic biomarker candidate based on its significantly increased abundance in the late-stage HGSOC patient sera compared to the healthy controls and patients with benign ovarian conditions. CONCLUSIONS A multiplexed targeted PRM MS assay was applied to detect candidate diagnostic biomarkers in HGSOC sera. To evaluate the clinical utility of the IBP2 PRM assay for HGSOC detection, further studies need to be performed using a larger patient cohort.
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Affiliation(s)
- Joohyun Ryu
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Kristin L M Boylan
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Carly A I Twigg
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Richard Evans
- Clinical and Translational Research Institute, University of Minnesota, Minneapolis, MN, USA
| | - Amy P N Skubitz
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Stefani N Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, USA.
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4
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Juanes-Velasco P, Arias-Hidalgo C, Landeira-Viñuela A, Nuño-Soriano A, Fuentes-Vacas M, Góngora R, Hernández ÁP, Fuentes M. Functional proteomics based on protein microarray technology for biomedical research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:49-65. [PMID: 38220432 DOI: 10.1016/bs.apcsb.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
This chapter traces a route through Proteomics from its origins to the present day. The different proteomics applications are discussed with a focus on microarray technology. Analytical microarrays, functional microarrays and reverse phase microarrays and their different applications are discussed. Several studies are mentioned where the great versatility of this approach is shown. Finally, the advantages and future challenges of microarray technology are outlined.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ana Nuño-Soriano
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina Fuentes-Vacas
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafa Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.
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5
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Chen Z, Leung TCN, Lui YL, Ngai SM, Chung HY. Combination of untargeted and targeted proteomics for secretome analysis of L-WRN cells. Anal Bioanal Chem 2023; 415:1465-1476. [PMID: 36656349 DOI: 10.1007/s00216-023-04534-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/25/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023]
Abstract
Organoid culture is a promising biomedical technology that requires specialized growth factors. Recently, a recombinant L-WRN cell line has been extensively used to generate conditioned medium (L-CM) for organoid culture. Nevertheless, methods for evaluating the stability of the L-WRN cells have been limited. In this study, a novel proteomics-based approach was developed to analyze the secretome of the cells. Serum-free L-CM was lyophilized, precipitated by trichloroacetic acid, and desalted prior to analysis by liquid chromatography-tandem mass spectrometry. Data-dependent acquisition (DDA) was conducted for the untargeted secretome profiling of the cells, and parallel reaction monitoring (PRM) was applied for the targeted quantification of the Wnt3A, R-spondin3, and noggin proteins (WRNs). This study also compared the performance of two types of PRM methods, namely MS1-independent PRM and MS1-dependent PRM, that can be executed on an Orbitrap instrument. The results showed that the growth of mouse intestinal organoids was closely related to the use of L-CM. The composition of L-CM could be markedly affected by the medium collection scheme. A total of 1725, 2302, and 2681 proteins were identified from the L-CM collected on day 5, day 9, and day 13, respectively. The MS1-independent PRM outperformed the MS1-dependent PRM and effectively quantified the WRNs with high repeatability and specificity. In conclusion, by integrating untargeted and targeted proteomics, this study develops a mass spectrometry-based method for the secretome analysis and quality control of the L-WRN cells. The methodology and findings of the present work will benefit future studies on organoids and secretomes.
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Affiliation(s)
- Zixing Chen
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Thomas Chun Ning Leung
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Ying Lam Lui
- Cell and Molecular Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Sai Ming Ngai
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hau Yin Chung
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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6
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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7
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Ives A, Dunn HA, Afsari HS, Seckler HDS, Foroutan MJ, Chavez E, Melani RD, Fellers RT, LeDuc RD, Thomas PM, Martemyanov KA, Kelleher NL, Vafabakhsh R. Middle-Down Mass Spectrometry Reveals Activity-Modifying Phosphorylation Barcode in a Class C G Protein-Coupled Receptor. J Am Chem Soc 2022; 144:23104-23114. [PMID: 36475650 PMCID: PMC9785046 DOI: 10.1021/jacs.2c10697] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane receptors in humans. They mediate nearly all aspects of human physiology and thus are of high therapeutic interest. GPCR signaling is regulated in space and time by receptor phosphorylation. It is believed that different phosphorylation states are possible for a single receptor, and each encodes for unique signaling outcomes. Methods to determine the phosphorylation status of GPCRs are critical for understanding receptor physiology and signaling properties of GPCR ligands and therapeutics. However, common proteomic techniques have provided limited quantitative information regarding total receptor phosphorylation stoichiometry, relative abundances of isomeric modification states, and temporal dynamics of these parameters. Here, we report a novel middle-down proteomic strategy and parallel reaction monitoring (PRM) to quantify the phosphorylation states of the C-terminal tail of metabotropic glutamate receptor 2 (mGluR2). By this approach, we found that mGluR2 is subject to both basal and agonist-induced phosphorylation at up to four simultaneous sites with varying probability. Using a PRM tandem mass spectrometry methodology, we localized the positions and quantified the relative abundance of phosphorylations following treatment with an agonist. Our analysis showed that phosphorylation within specific regions of the C-terminal tail of mGluR2 is sensitive to receptor activation, and subsequent site-directed mutagenesis of these sites identified key regions which tune receptor sensitivity. This study demonstrates that middle-down purification followed by label-free quantification is a powerful, quantitative, and accessible tool for characterizing phosphorylation states of GPCRs and other challenging proteins.
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Affiliation(s)
- Ashley
N. Ives
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208 United States
| | - Henry A. Dunn
- Department
of Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States,Department
of Pharmacology and Therapeutics, University
of Manitoba, Winnipeg, Manitoba R3E 0T6, Canada,Division
of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen
Research Centre, Winnipeg, Manitoba R2H 2A6, Canada
| | - Hamid Samareh Afsari
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | | | - Max J. Foroutan
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Erica Chavez
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Ryan T. Fellers
- National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard D. LeDuc
- National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Paul M. Thomas
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Kirill A. Martemyanov
- Department
of Neuroscience, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Neil L. Kelleher
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208 United States,Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,National
Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Reza Vafabakhsh
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,
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Banerjee A, Biswas D, Barpanda A, Halder A, Sibal S, Kattimani R, Shah A, Mahadevan A, Goel A, Srivastava S. The First Pituitary Proteome Landscape From Matched Anterior and Posterior Lobes for a Better Understanding of the Pituitary Gland. Mol Cell Proteomics 2022; 22:100478. [PMID: 36470533 PMCID: PMC9877467 DOI: 10.1016/j.mcpro.2022.100478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
To date, very few mass spectrometry (MS)-based proteomics studies are available on the anterior and posterior lobes of the pituitary. In the past, MS-based investigations have focused exclusively on the whole pituitary gland or anterior pituitary lobe. In this study, for the first time, we performed a deep MS-based analysis of five anterior and five posterior matched lobes to build the first lobe-specific pituitary proteome map, which documented 4090 proteins with isoforms, mostly mapped into chromosomes 1, 2, and 11. About 1446 differentially expressed significant proteins were identified, which were studied for lobe specificity, biological pathway enrichment, protein-protein interaction, regions specific to comparison of human brain and other neuroendocrine glands from Human Protein Atlas to identify pituitary-enriched proteins. Hormones specific to each lobe were also identified and validated with parallel reaction monitoring-based target verification. The study identified and validated hormones, growth hormone and thyroid-stimulating hormone subunit beta, exclusively to the anterior lobe whereas oxytocin-neurophysin 1 and arginine vasopressin to the posterior lobe. The study also identified proteins POU1F1 (pituitary-specific positive transcription factor 1), POMC (pro-opiomelanocortin), PCOLCE2 (procollagen C-endopeptidase enhancer 2), and NPTX2 (neuronal pentraxin-2) as pituitary-enriched proteins and was validated for their lobe specificity using parallel reaction monitoring. In addition, three uPE1 proteins, namely THEM6 (mesenchymal stem cell protein DSCD75), FSD1L (coiled-coil domain-containing protein 10), and METTL26 (methyltransferase-like 26), were identified using the NeXtProt database, and depicted tumor markers S100 proteins having high expression in the posterior lobe. In summary, the study documents the first matched anterior and posterior pituitary proteome map acting as a reference control for a better understanding of functional and nonfunctional pituitary adenomas and extrapolating the aim of the Human Proteome Project towards the investigation of the proteome of life.
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Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deepatarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Shamira Sibal
- Lokmanya Tilak Municipal Medical College, Mumbai, India
| | | | - Abhidha Shah
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Anita Mahadevan
- Human Brain Bank, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Atul Goel
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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9
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Steiner C, Lescuyer P, Cutler P, Tille JC, Ducret A. Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays. Mol Cell Proteomics 2022; 21:100416. [PMID: 36152753 PMCID: PMC9638817 DOI: 10.1016/j.mcpro.2022.100416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 01/18/2023] Open
Abstract
The identification of clinically relevant biomarkers represents an important challenge in oncology. This problem can be addressed with biomarker discovery and verification studies performed directly in tumor samples using formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring proteins in FFPE samples remains challenging. Here, we demonstrate the use of liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM/MS) as an effective technique for such applications. An LC-MRM/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples and was applied to the targeted measurement of 200 proteins in 48 triple-negative, 19 HER2-overexpressing, and 20 luminal A breast tumors. Quantitative information was obtained for 185 proteins, including known markers of breast cancer such as HER2, hormone receptors, Ki-67, or inflammation-related proteins. LC-MRM/MS results for these proteins matched immunohistochemistry or chromogenic in situ hybridization data. In addition, comparison of our results with data from the literature showed that several proteins representing potential biomarkers were identified as differentially expressed in triple-negative breast cancer samples. These results indicate that LC-MRM/MS assays can reliably measure large sets of proteins using the analysis of surrogate peptides extracted from FFPE samples. This approach allows to simultaneously quantify the expression of target proteins from various pathways in tumor samples. LC-MRM/MS is thus a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.
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Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland,BiOmics and Pathology, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Switzerland,For correspondence: Carine Steiner
| | - Pierre Lescuyer
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland,Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Paul Cutler
- BiOmics and Pathology, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Switzerland
| | - Jean-Christophe Tille
- Division of Clinical Pathology, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - Axel Ducret
- BiOmics and Pathology, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Switzerland
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10
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Jiang J, Zhao J, Wang Y, Liu D, Zhang M. Urine inter‐alpha‐trypsin inhibitor family‐related proteins may serve as biomarkers for disease activity of lupus. J Clin Lab Anal 2022; 36:e24622. [PMID: 35870194 PMCID: PMC9459346 DOI: 10.1002/jcla.24622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a chronic inflammatory disease involving multiple tissues. Inter‐Alpha‐Trypsin Inhibitor (ITI) family proteins have a role in maintaining tissue homeostasis, but their possible clinical significance in the SLE patients has not been reported. The aim of this study was to analyze and verify the expression of ITI‐related proteins in the urine of SLE patients, further explore the features of these proteins in disease activity. Methods Based on label‐free proteomics technology and bioinformatics technology, we analyzed the expression of ITI family‐related proteins in the urine of lupus. Subsequently, Western‐blot and targeted proteomics were used to qualitatively and quantitatively verify the expression of these proteins, respectively. Results A total of seven ITI family‐related proteins were screened and identified; and six of these proteins were differentially expressed in the urine of SLE patients. Further quantitative analysis showed that the expressions of ITIH2, ECM1, and ITIH5 in urine between active SLE group and stable SLE group were consistent with the preliminary screening results. The expression of ITIH2 and ECM1 in the renal damage group were also consistent with the screening results. Moreover, ITIH2 and ECM1 have a good correlation with disease activity and have a certain correlation with renal damage. Conclusions In this exploratory study, we evaluated the expression of ITI family‐related proteins in the urine of SLE and found that urine ITIH2 and ECM1 were closely related to SLE activity, especially kidney damage, providing an experimental basis for further exploration of the potential roles in monitoring lupus and lupus nephritis activity.
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Affiliation(s)
- Jun Jiang
- Clinical Laboratory Medicine Peking University Ninth School of Clinical Medicine Beijing China
| | - Jin Zhao
- Clinical Laboratory Medicine, Beijing Shijitan Hospital Capital Medical University Beijing China
| | - Yuhua Wang
- Department of Rheumatology and Clinical Immunology, Beijing Shijitan Hospital Capital Medical University Beijing China
| | - Dan Liu
- Clinical Laboratory Medicine Peking University Ninth School of Clinical Medicine Beijing China
| | - Man Zhang
- Clinical Laboratory Medicine Peking University Ninth School of Clinical Medicine Beijing China
- Clinical Laboratory Medicine, Beijing Shijitan Hospital Capital Medical University Beijing China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics Beijing China
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Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT-474 breast cancer cell line. Clin Proteomics 2022; 19:14. [PMID: 35568821 PMCID: PMC9107748 DOI: 10.1186/s12014-022-09352-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Accumulating evidence suggests that the androgen receptor (AR) and its endogenous ligands influence disease progression in breast cancer (BCa). However, AR-mediated changes in BCa differ among the various BCa subtypes according to their hormone receptor profile [i.e., presence/absence of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2, (HER2)]. Thus, we explored the androgen-regulated transcriptomic changes in the ER+PR+HER2+ BCa cell line, BT-474, and compared them with PR-mediated changes. METHODS We performed RNA sequencing analysis in treated BT-474 cells with dihydrotestosterone (DHT) and progesterone. Validation of the top ten differentially androgen-regulated genes and a number of other genes found in enriched signaling pathways was performed by qRT-PCR in BT-474 and other BCa cell lines. In addition, a parallel reaction monitoring targeted proteomic approach was developed to verify selected transcripts at the protein level. RESULTS In total 19,450 transcripts were detected, of which 224 were differentially regulated after DHT treatment. The increased expression of two well-known androgen-regulated genes, KLK2 (p < 0.05) and KLK3 (p < 0.001), confirmed the successful androgen stimulation in BT-474 cells. The transcription factor, ZBTB16, was the most highly upregulated gene, with ~ 1000-fold change (p < 0.001). Pathway enrichment analysis revealed downregulation of the DNA replication processes (p < 0.05) and upregulation of the androgen signaling and fatty acid metabolism pathways (p < 0.05). Changes related to progesterone treatment showed opposite effects in gene expression than DHT treatment. Similar expression profiles were observed among other BCa cell lines expressing high levels of AR (ZR75.1 and MBA-MB-453). The parallel reaction monitoring targeted proteomic analysis further confirmed that altered protein expression (KLK3, ALOX15B) in the supernatant and cell lysate of DHT-treated BT-474 cells, compared to control cells. DISCUSSION Our findings suggest that AR modulates the metabolism of BT-474 cells by affecting the expression of a large number of genes and proteins. Based on further pathway analysis, we suggest that androgen receptor acts as a tumor suppressor in the BT-474 cells.
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Liu X, Li X, Chen L, Hsu ACY, Asquith KL, Liu C, Laurie K, Barr I, Foster PS, Yang M. Proteomic Analysis Reveals a Novel Therapeutic Strategy Using Fludarabine for Steroid-Resistant Asthma Exacerbation. Front Immunol 2022; 13:805558. [PMID: 35280986 PMCID: PMC8913936 DOI: 10.3389/fimmu.2022.805558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/04/2022] [Indexed: 11/30/2022] Open
Abstract
Virus-induced asthma exacerbation is a health burden worldwide and lacks effective treatment. To better understand the disease pathogenesis and find novel therapeutic targets, we established a mouse model of steroid (dexamethasone (DEX)) resistant asthma exacerbation using ovalbumin (OVA) and influenza virus (FLU) infection. Using liquid chromatography-tandem mass spectrometry (LC-MC/MS), we performed a shotgun proteomics assay coupled with label-free quantification to define all dysregulated proteins in the lung proteome of asthmatic mice. Compared to control, 71, 89, and 30 proteins were found significantly upregulated by at least two-fold (p-value ≤ 0.05) in OVA-, OVA/FLU-, and OVA/FLU/DEX-treated mice, respectively. We then applied a Z-score transformed hierarchical clustering analysis and Ingenuity Pathway Analysis (IPA) to highlight the key inflammation pathways underlying the disease. Within all these upregulated proteins, 64 proteins were uniquely highly expressed in OVA/FLU mice compared to OVA mice; and 11 proteins were DEX-refractory. IPA assay revealed two of the most enriched pathways associated with these over-expressed protein clusters were those associated with MHC class I (MHC-I) antigen-presentation and interferon (IFN) signaling. Within these pathways, signal-transducer-and-activator-of-transcription-1 (STAT1) protein was identified as the most significantly changed protein contributing to the pathogenesis of exacerbation and the underlying steroid resistance based on the label-free quantification; and this was further confirmed by both Parallel Reaction Monitoring (PRM) proteomics assay and western blots. Further, the pharmacological drug Fludarabine decreased STAT1 expression, restored the responsiveness of OVA/FLU mice to DEX and markedly suppressed disease severity. Taken together, this study describes the proteomic profile underpinning molecular mechanisms of FLU-induced asthma exacerbation and identifies STAT1 as a potential therapeutic target, more importantly, we provided a novel therapeutic strategy that may be clinically translated into practice.
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Affiliation(s)
- Xiaoming Liu
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Health Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia
| | - Xiang Li
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Health Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia
| | - Ling Chen
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Health Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia
| | - Alan Chen-Yu Hsu
- Priority Research Centre for Health Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Kelly L. Asquith
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Health Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia
| | - Chi Liu
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Karen Laurie
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Paul S. Foster
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Health Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia
- *Correspondence: Ming Yang, ; Paul S. Foster,
| | - Ming Yang
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Health Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia
- *Correspondence: Ming Yang, ; Paul S. Foster,
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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Escobar EE, Venkat Ramani MK, Zhang Y, Brodbelt JS. Evaluating Spatiotemporal Dynamics of Phosphorylation of RNA Polymerase II Carboxy-Terminal Domain by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2021; 143:8488-8498. [PMID: 34053220 DOI: 10.1021/jacs.1c03321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The critical role of site-specific phosphorylation in eukaryotic transcription has motivated efforts to decipher the complex phosphorylation patterns exhibited by the carboxyl-terminal domain (CTD) of RNA polymerase II. Phosphorylation remains a challenging post-translational modification to characterize by mass spectrometry owing to the labile phosphate ester linkage and low stoichiometric prevalence, two features that complicate analysis by high-throughput MS/MS methods. Identifying phosphorylation sites represents one significant hurdle in decrypting the CTD phosphorylation, a problem exaggerated by a large number of potential phosphorylation sites. An even greater obstacle is decoding the dynamic phosphorylation pattern along the length of the periodic CTD sequence. Ultraviolet photodissociation (UVPD) is a high-energy ion activation method that provides ample backbone cleavages of peptides while preserving labile post-translational modifications that facilitate their confident localization. Herein, we report a quantitative parallel reaction monitoring (PRM) method developed to monitor spatiotemporal changes in site-specific Ser5 phosphorylation of the CTD by cyclin-dependent kinase 7 (CDK7) using UVPD for sequence identification, phosphosite localization, and differentiation of phosphopeptide isomers. We capitalize on the series of phospho-retaining fragment ions produced by UVPD to create unique transition lists that are pivotal for distinguishing the array of phosphopeptides generated from the CTD.
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Qi P, Zhou QQ, Lin ZH, Liu J, Cai WY, Mao XW, Jiang JJ. Qualitative screening and quantitative determination of multiclass water-soluble synthetic dyes in foodstuffs by liquid chromatography coupled to quadrupole Orbitrap mass spectrometry. Food Chem 2021; 360:129948. [PMID: 33975070 DOI: 10.1016/j.foodchem.2021.129948] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/31/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022]
Abstract
A LC-Q-Orbitrap HRMS analytical method for both qualitative screening and quantitative determination of 90 synthetic dyes including ten groups of isomers in foods has been established. An in-house synthetic dyes database and characteristic ions were also developed. Based on Q-Orbitrap HRMS, mass spectrum and fragmentation patterns of synthetic dyes were studied, which indicated that double charged ions were usually the main precursor ions. Matrix effects were successfully eliminated by the C18 d-SPE clean-up coupled with dilute and shoot approach with methanol-water (1:4, v/v) in 100-fold. For most of the compounds, mean recoveries were satisfactory between 70% and 120% with RSD < 20% at three spiked level in the range of 0.025-1.0 mg/kg. The screening detection limits ranged from 0.025 - 1.0 mg/kg. Method validation showed that the established method was efficient, rapid and high-throughput, which has been successfully applied to the monitoring of these water-soluble synthetic dyes in foods.
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Affiliation(s)
- Ping Qi
- Guang Zhou Institute for Food Inspection, Guangzhou 511410, China
| | - Qiong-Qing Zhou
- Guang Zhou Institute for Food Inspection, Guangzhou 511410, China
| | - Zi-Hao Lin
- Guang Zhou Institute for Food Inspection, Guangzhou 511410, China
| | - Jia Liu
- Guang Zhou Institute for Food Inspection, Guangzhou 511410, China
| | - Wei-Yi Cai
- Guang Zhou Institute for Food Inspection, Guangzhou 511410, China
| | - Xin-Wu Mao
- Guang Zhou Institute for Food Inspection, Guangzhou 511410, China.
| | - Ji-Jun Jiang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China.
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