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Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
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Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
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2
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Lee CC, Lin YC, Pan TY, Yang CH, Li PH, Chen SY, Gao JJ, Yang C, Chu LJ, Huang PJ, Yeh YM, Tang P, Chang YS, Yu JS, Hsiao YC. HeapMS: An Automatic Peak-Picking Pipeline for Targeted Proteomic Data Powered by 2D Heatmap Transformation and Convolutional Neural Networks. Anal Chem 2023; 95:15486-15496. [PMID: 37820297 PMCID: PMC10603604 DOI: 10.1021/acs.analchem.3c01011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
The process of peak picking and quality assessment for multiple reaction monitoring (MRM) data demands significant human effort, especially for signals with low abundance and high interference. Although multiple peak-picking software packages are available, they often fail to detect peaks with low quality and do not report cases with low confidence. Furthermore, visual examination of all chromatograms is still necessary to identify uncertain or erroneous cases. This study introduces HeapMS, a web service that uses artificial intelligence to assist with peak picking and the quality assessment of MRM chromatograms. HeapMS applies a rule-based filter to remove chromatograms with low interference and high-confidence peak boundaries detected by Skyline. Additionally, it transforms two histograms (representing light and heavy peptides) into a single encoded heatmap and performs a two-step evaluation (quality detection and peak picking) using image convolutional neural networks. HeapMS offers three categories of peak picking: uncertain peak picking that requires manual inspection, deletion peak picking that requires removal or manual re-examination, and automatic peak picking. HeapMS acquires the chromatogram and peak-picking boundaries directly from Skyline output. The output results are imported back into Skyline for further manual inspection, facilitating integration with Skyline. HeapMS offers the benefit of detecting chromatograms that should be deleted or require human inspection. Based on defined categories, it can significantly reduce human workload and provide consistent results. Furthermore, by using heatmaps instead of histograms, HeapMS can adapt to future updates in image recognition models. The HeapMS is available at: https://github.com/ccllabe/HeapMS.
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Affiliation(s)
- Chi-Ching Lee
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
- Artificial
Intelligence Research Center, Chang Gung
University, 33302 Taoyuan, Taiwan
| | - Yu-Chieh Lin
- Graduate
Institute of Artificial Intelligence, Chang
Gung University, 33302 Taoyuan, Taiwan
| | - Teng Yu Pan
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Cheng Hann Yang
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Pei-Hsuan Li
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Sin You Chen
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
- Artificial
Intelligence Research Center, Chang Gung
University, 33302 Taoyuan, Taiwan
| | - Jhih Jie Gao
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Chi Yang
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Lichieh Julie Chu
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
| | - Po-Jung Huang
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
- Department
of Biomedical Sciences, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
| | - Petrus Tang
- Molecular
Infectious Disease Research Center, Chang
Gung Memorial Hospital, 33305 Taoyuan, Taiwan
- Department
of Parasitology, College of Medicine, Chang
Gung University, 33302 Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Jau-Song Yu
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
- Research
Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, 33302 Taoyuan, Taiwan
| | - Yung-Chin Hsiao
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
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Abstract
INTRODUCTION Due to its excellent sensitivity, nano-flow liquid chromatography tandem mass spectrometry (LC-MS/MS) is the mainstay in proteome research; however, this comes at the expense of limited throughput and robustness. In contrast, micro-flow LC-MS/MS enables high-throughput, robustness, quantitative reproducibility, and precision while retaining a moderate degree of sensitivity. Such features make it an attractive technology for a wide range of proteomic applications. In particular, large-scale projects involving the analysis of hundreds to thousands of samples. AREAS COVERED This review summarizes the history of chromatographic separation in discovery proteomics with a focus on micro-flow LC-MS/MS, discusses the current state-of-the-art, highlights advances in column development and instrumentation, and provides guidance on which LC flow best supports different types of proteomic applications. EXPERT OPINION Micro-flow LC-MS/MS will replace nano-flow LC-MS/MS in many proteomic applications, particularly when sample quantities are not limited and sample cohorts are large. Examples include clinical analyses of body fluids, tissues, drug discovery and chemical biology investigations, plus systems biology projects across all kingdoms of life. When combined with rapid and sensitive MS, intelligent data acquisition, and informatics approaches, it will soon become possible to analyze large cohorts of more than 10,000 samples in a comprehensive and fully quantitative fashion.
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Affiliation(s)
- Yangyang Bian
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Chunli Gao
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
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Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS. Nat Commun 2020; 11:157. [PMID: 31919466 PMCID: PMC6952431 DOI: 10.1038/s41467-019-13973-x] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023] Open
Abstract
Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC–MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness. Here we show that micro-flow LC–MS/MS using a 1 × 150 mm column shows excellent reproducibility of chromatographic retention time (<0.3% coefficient of variation, CV) and protein quantification (<7.5% CV) using data from >2000 samples of human cell lines, tissues and body fluids. Deep proteome analysis identifies >9000 proteins and >120,000 peptides in 16 h and sample multiplexing using tandem mass tags increases throughput to 11 proteomes in 16 h. The system identifies >30,000 phosphopeptides in 12 h and protein-protein or protein-drug interaction experiments can be analyzed in 20 min per sample. We show that the same column can be used to analyze >7500 samples without apparent loss of performance. This study demonstrates that micro-flow LC–MS/MS is suitable for a broad range of proteomic applications. Mass spectrometry-based proteomics typically relies on highly sensitive nano-flow liquid chromatography (LC) but this can reduce robustness and reproducibility. Here, the authors show that micro-flow LC enables robust and reproducible high-throughput proteomics experiments at a very moderate loss of sensitivity.
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5
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Assessment of candidate biomarkers in paired saliva and plasma samples from oral cancer patients by targeted mass spectrometry. J Proteomics 2020; 211:103571. [DOI: 10.1016/j.jprot.2019.103571] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/26/2019] [Accepted: 10/30/2019] [Indexed: 12/29/2022]
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Distler U, Łącki MK, Schumann S, Wanninger M, Tenzer S. Enhancing Sensitivity of Microflow-Based Bottom-Up Proteomics through Postcolumn Solvent Addition. Anal Chem 2019; 91:7510-7515. [PMID: 31117400 DOI: 10.1021/acs.analchem.9b00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The introduction of more sensitive mass spectrometers allows researchers to adapt front-end liquid chromatography (LC) to individual needs for the analysis of complex proteomes. Where absolute sensitivity is not paramount, it is advantageous to switch from a highly sensitive nanoflow-LC setup, the de facto standard platform in mass-spectrometry (MS)-based discovery proteomics, to a more robust, high-throughput-compatible microflow or conventional-flow setup. To enhance the microflow-LC-MS electrospray process of complex proteomic samples, we tested the effects of different solvents, including 2-propanol, methanol, and acetonitrile, pure or as mixture with dimethyl sulfoxide, which were added postcolumn to the eluting sample. Postcolumn addition of organic solvents strongly enhanced the electrospray efficiency in microflow-LC-MS experiments and improved the sensitivity across the entire gradient and for early eluting peptides by up to 10-fold. Postcolumn solvent addition did not negatively affect chromatographic performance and resulted in an overall 28-36% increase in identifications at both the protein and peptide levels. The presented microflow-LC-MS workflow, including postcolumn solvent addition, can be easily adopted on any LC-MS/MS platform.
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Affiliation(s)
- Ute Distler
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany.,Focus Program Translational Neuroscience (FTN) , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
| | - Sven Schumann
- Institute of Anatomy , Otto von Guericke University Magdeburg , Magdeburg 39120 , Germany
| | - Markus Wanninger
- Waters Corporation , Milford , Massachusetts 01757 , United States
| | - Stefan Tenzer
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
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7
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Lenčo J, Vajrychová M, Pimková K, Prokšová M, Benková M, Klimentová J, Tambor V, Soukup O. Conventional-Flow Liquid Chromatography-Mass Spectrometry for Exploratory Bottom-Up Proteomic Analyses. Anal Chem 2018; 90:5381-5389. [PMID: 29582996 DOI: 10.1021/acs.analchem.8b00525] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Due to its sensitivity and productivity, bottom-up proteomics based on liquid chromatography-mass spectrometry (LC-MS) has become the core approach in the field. The de facto standard LC-MS platform for proteomics operates at sub-μL/min flow rates, and nanospray is required for efficiently introducing peptides into a mass spectrometer. Although this is almost a "dogma", this view is being reconsidered in light of developments in highly efficient chromatographic columns, and especially with the introduction of exceptionally sensitive MS instruments. Although conventional-flow LC-MS platforms have recently penetrated targeted proteomics successfully, their possibilities in discovery-oriented proteomics have not yet been thoroughly explored. Our objective was to determine what are the extra costs and what optimization and adjustments to a conventional-flow LC-MS system must be undertaken to identify a comparable number of proteins as can be identified on a nanoLC-MS system. We demonstrate that the amount of a complex tryptic digest needed for comparable proteome coverage can be roughly 5-fold greater, providing the column dimensions are properly chosen, extra-column peak dispersion is minimized, column temperature and flow rate are set to levels appropriate for peptide separation, and the composition of mobile phases is fine-tuned. Indeed, we identified 2 835 proteins from 2 μg of HeLa cells tryptic digest separated during a 60 min gradient at 68 μL/min on a 1.0 mm × 250 mm column held at 55 °C and using an aqua-acetonitrile mobile phases containing 0.1% formic acid, 0.4% acetic acid, and 3% dimethyl sulfoxide. Our results document that conventional-flow LC-MS is an attractive alternative for bottom-up exploratory proteomics.
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Affiliation(s)
- Juraj Lenčo
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic.,Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic.,Department of Analytical Chemistry, Faculty of Pharmacy , Charles University in Prague , Heyrovského 1203 , 500 05 Hra-dec Králové , Czech Republic
| | - Marie Vajrychová
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic.,Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic
| | - Kristýna Pimková
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
| | - Magdaléna Prokšová
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic
| | - Markéta Benková
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
| | - Jana Klimentová
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic
| | - Vojtěch Tambor
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
| | - Ondřej Soukup
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
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8
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Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Öztürk VÖ, Afacan B, Emingil G, Belibasakis GN. Targeted Proteomics Guided by Label-free Quantitative Proteome Analysis in Saliva Reveal Transition Signatures from Health to Periodontal Disease. Mol Cell Proteomics 2018; 17:1392-1409. [PMID: 29610270 DOI: 10.1074/mcp.ra118.000718] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/28/2018] [Indexed: 12/18/2022] Open
Abstract
Periodontal diseases are among the most prevalent worldwide, but largely silent, chronic diseases. They affect the tooth-supporting tissues with multiple ramifications on life quality. Their early diagnosis is still challenging, due to lack of appropriate molecular diagnostic methods. Saliva offers a non-invasively collectable reservoir of clinically relevant biomarkers, which, if utilized efficiently, could facilitate early diagnosis and monitoring of ongoing disease. Despite several novel protein markers being recently enlisted by discovery proteomics, their routine diagnostic application is hampered by the lack of validation platforms that allow for rapid, accurate and simultaneous quantification of multiple proteins in large cohorts. Here we carried out a pipeline of two proteomic platforms; firstly, we applied open ended label-free quantitative (LFQ) proteomics for discovery in saliva (n = 67, including individuals with health, gingivitis, and periodontitis), followed by selected-reaction monitoring (SRM)-targeted proteomics for validation in an independent cohort (n = 82). The LFQ platform led to the discovery of 119 proteins with at least 2-fold significant difference between health and disease. The 65 proteins chosen for the subsequent SRM platform included 50 functionally related proteins derived from the significantly enriched processes of the LFQ data, 11 from literature-mining, and four house-keeping ones. Among those, 60 were reproducibly quantifiable proteins (92% success rate), represented by a total of 143 peptides. Machine-learning modeling led to a narrowed-down panel of five proteins of high predictive value for periodontal diseases with maximum area under the receiver operating curve >0.97 (higher in disease: Matrix metalloproteinase-9, Ras-related protein-1, Actin-related protein 2/3 complex subunit 5; lower in disease: Clusterin, Deleted in Malignant Brain Tumors 1). This panel enriches the pool of credible clinical biomarker candidates for diagnostic assay development. Yet, the quantum leap brought into the field of periodontal diagnostics by this study is the application of the biomarker discovery-through-verification pipeline, which can be used for validation in further cohorts.
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Affiliation(s)
- Nagihan Bostanci
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden;
| | - Nathalie Selevsek
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Witold Wolski
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Kai Bao
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Asa Wahlander
- ¶AstraZeneca Translational Biomarkers and Bioanalysis, Drug Safety and Metabolism, Innovative Medicines, Mölndal, Sweden
| | - Christian Trachsel
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Ralph Schlapbach
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Veli Özgen Öztürk
- ‖Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydin, Turkey
| | - Beral Afacan
- ‖Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydin, Turkey
| | - Gulnur Emingil
- **Department of Periodontology, School of Dentistry, Ege University, Izmir, Turkey
| | - Georgios N Belibasakis
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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9
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Hsiao YC, Chu LJ, Chen YT, Chi LM, Chien KY, Chiang WF, Chang YT, Chen SF, Wang WS, Chuang YN, Lin SY, Chien CY, Chang KP, Chang YS, Yu JS. Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring-Mass Spectrometry. Proteomics Clin Appl 2018; 12. [PMID: 29350471 DOI: 10.1002/prca.201700039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/11/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE Saliva is an attractive sample source for the biomarker-based testing of several diseases, especially oral cancer. Here, we sought to apply multiplexed LC-MRM-MS to precisely quantify 90 disease-related proteins and assess their intra- and interindividual variability in saliva samples from healthy donors. EXPERIMENTAL DESIGN We developed two multiplexed LC-MRM-MS assays for 122 surrogate peptides representing a set of disease-related proteins. Saliva samples were collected from 10 healthy volunteers at three different time points (Day 1 morning and afternoon, and Day 2 morning). Each sample was spiked with a constant amount of a 15 N-labeled protein and analyzed by MRM-MS in triplicate. Quantitative results from LC-MRM-MS were calculated by single-point quantification with reference to a known amount of internal standard (heavy peptide). RESULTS The CVs for assay reproducibility and technical variation were 13 and 11%, respectively. The average concentrations of the 99 successfully quantified proteins ranged from 0.28 ± 0.58 ng mL-1 for profilin-2 (PFN2) to 8.55 ±8.96 μg mL-1 for calprotectin (S100A8). For the 90 proteins detectable in >50% of samples, the average CVs for intraday, interday, intraindividual, and interindividual samples were 38%, 43%, 45%, and 69%, respectively. The fluctuations of most target proteins in individual subjects were found to be within ± twofold. CONCLUSIONS AND CLINICAL RELEVANCE Our study elucidated the intra- and interindividual variability of 90 disease-related proteins in saliva samples from healthy donors. The findings may facilitate the further development of salivary biomarkers for oral and systemic diseases.
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Affiliation(s)
- Yung-Chin Hsiao
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lang-Ming Chi
- Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kun-Yi Chien
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Fan Chiang
- Department of Oral and Maxillofacial Surgery, Chi-Mei Medical Center, Tainan, Taiwan.,School of Dentistry, National Yang Ming University, Taipei, Taiwan
| | - Ya-Ting Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Szu-Fan Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Shun Wang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yao-Ning Chuang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Yu Lin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Yen Chien
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Ping Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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10
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Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. Sci Data 2017; 4:170091. [PMID: 28722704 PMCID: PMC5516542 DOI: 10.1038/sdata.2017.91] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 06/01/2017] [Indexed: 02/06/2023] Open
Abstract
Mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are emerging as a promising tool for verification of candidate proteins in biological and biomedical applications. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large sets of targeted MS-based assays, and a depository to share assays publicly. Herein, we report the development of 98 SRM assays that have been thoroughly characterized according to the CPTAC Assay Characterization Guidance Document; 37 of these passed all five experimental tests. The assays cover 70 proteins previously identified at the protein level in ovarian tumors. The experiments, methods and results for characterizing these SRM assays for their MS response, repeatability, selectivity, stability, and endogenous detection are described in detail. Data are available via PeptideAtlas, Panorama and the CPTAC Assay Portal.
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11
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Chen YT, Chen HW, Wu CF, Chu LJ, Chiang WF, Wu CC, Yu JS, Tsai CH, Liang KH, Chang YS, Wu M, Ou Yang WT. Development of a Multiplexed Liquid Chromatography Multiple-Reaction-Monitoring Mass Spectrometry (LC-MRM/MS) Method for Evaluation of Salivary Proteins as Oral Cancer Biomarkers. Mol Cell Proteomics 2017; 16:799-811. [PMID: 28235782 PMCID: PMC5417822 DOI: 10.1074/mcp.m116.064758] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 02/22/2017] [Indexed: 11/06/2022] Open
Abstract
Multiple (selected) reaction monitoring (MRM/SRM) of peptides is a growing technology for target protein quantification because it is more robust, precise, accurate, high-throughput, and multiplex-capable than antibody-based techniques. The technique has been applied clinically to the large-scale quantification of multiple target proteins in different types of fluids. However, previous MRM-based studies have placed less focus on sample-preparation workflow and analytical performance in the precise quantification of proteins in saliva, a noninvasively sampled body fluid. In this study, we evaluated the analytical performance of a simple and robust multiple reaction monitoring (MRM)-based targeted proteomics approach incorporating liquid chromatography with mass spectrometry detection (LC-MRM/MS). This platform was used to quantitatively assess the biomarker potential of a group of 56 salivary proteins that have previously been associated with human cancers. To further enhance the development of this technology for assay of salivary samples, we optimized the workflow for salivary protein digestion and evaluated quantification performance, robustness and technical limitations in analyzing clinical samples. Using a clinically well-characterized cohort of two independent clinical sample sets (total n = 119), we quantitatively characterized these protein biomarker candidates in saliva specimens from controls and oral squamous cell carcinoma (OSCC) patients. The results clearly showed a significant elevation of most targeted proteins in saliva samples from OSCC patients compared with controls. Overall, this platform was capable of assaying the most highly multiplexed panel of salivary protein biomarkers, highlighting the clinical utility of MRM in oral cancer biomarker research.
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Affiliation(s)
- Yi-Ting Chen
- From the ‡Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan;
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- ‖Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Hsiao-Wei Chen
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Feng Wu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lichieh Julie Chu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- **Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wei-Fang Chiang
- ‡‡Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan
- §§School of Dentistry, National Yang Ming University, Taipei, Taiwan
| | - Chih-Ching Wu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶¶Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- ‖‖Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Jau-Song Yu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- **Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Cheng-Han Tsai
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kung-Hao Liang
- **Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yu-Sun Chang
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- ‖‖Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Maureen Wu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Ting Ou Yang
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
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