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Asicioglu M, Oztug M, Karaguler NG. Development of an ID-LC-MS/MS method using targeted proteomics for quantifying cardiac troponin I in human serum. Clin Proteomics 2023; 20:40. [PMID: 37759177 PMCID: PMC10536812 DOI: 10.1186/s12014-023-09430-z] [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: 06/16/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Cardiac troponin is a complex protein consisting of the three subunits I, T and C located in heart muscle cells. When the heart muscle is damaged, it is released into the blood and can be detected. Cardiac troponin I (cTnI) is considered the most reliable and widely accepted test for detecting and confirming acute myocardial infarction. However, there is no current standardization between the commercial assays for cTnI quantification. Our work aims to create a measurement procedure that is traceable to the International System of Units for accurately measuring cardiac cTnI levels in serum samples from patients. METHODS The workflow begins with immobilizing anti-cTnI antibodies onto magnetic nanoparticles to form complexes. These complexes are used to isolate cTnI from serum. Next, trypsin is used to enzymatically digest the isolated cTnI. Finally, the measurement of multiple cTnI peptides is done simultaneously using isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS). RESULTS The maximum antibody immobilization was achieved by combining 1 mg of nanoparticles with 100 μg of antibody, resulting in an average of 59.2 ± 5.7 μg/mg of immobilized antibody. Subsequently, the anti-cTnI-magnetic nanoparticle complex was utilized to develop and validate a method for quantifying cTnI in human serum using ID-LC-MS/MS and a protein calibration approach. The analytical method was assessed regarding linearity and recovery. The developed method enables the quantification of cTnI from 0.7 to 24 μg/L (R > 0.996). The limit of quantification was 1.8 μg/L and the limit of detection was 0.6 μg/L. Intermediate precision was ≤ 9.6% and repeatability was 2.0-8.7% for all quality control materials. The accuracy of the analyzed quality control materials was between 90 and 110%. Total measurement uncertainties for target value assignment (n = 6) were found to be ≤ 12.5% for all levels. CONCLUSIONS The analytical method demonstrated high analytical performance in accurately quantifying cardiac troponin I levels in human serum. The proposed analytical method has the potential to facilitate the harmonization of cTnI results between clinical laboratories, assign target values to secondary certified reference materials and support reliable measurement of cTnI.
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Affiliation(s)
- Meltem Asicioglu
- TUBITAK National Metrology Institute (TUBITAK UME), Gebze, 41400, Kocaeli, Turkey
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Ocalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul Technical University, Istanbul, Turkey
| | - Merve Oztug
- TUBITAK National Metrology Institute (TUBITAK UME), Gebze, 41400, Kocaeli, Turkey.
| | - Nevin Gul Karaguler
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Ocalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul Technical University, Istanbul, Turkey
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2
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Liu W, Wang Q, Chang J, Bhetuwal A, Bhattarai N, Zhang F, Tang J. Serum proteomics unveil characteristic protein diagnostic biomarkers and signaling pathways in patients with esophageal squamous cell carcinoma. Clin Proteomics 2022; 19:18. [PMID: 35610567 PMCID: PMC9128263 DOI: 10.1186/s12014-022-09357-x] [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: 01/29/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is a common digestive tract malignant tumor with high incidence and dismal prognosis worldwide. However, the reliable biomarkers for clinical diagnosis and the underlying signaling pathways insights of ESCC are not unequivocally understood yet. The serum proteome may provide valuable clues for the early diagnosis of ESCC and the discovery of novel molecular insights. Methods In the current study, an optimized proteomics approach was employed to discover novel serum-based biomarkers for ESCC, and unveil abnormal signal pathways. Gene ontology (GO) enrichment analysis was done by Gene Set Enrichment Analysis (GSEA) and Metascape database, respectively. Pathway analysis was accomplished by GeneCards database. The correlation coefficient was assessed using Pearson and distance correlation analyses. Prioritized candidates were further verified in two independent validation sets by enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry (IHC) staining. Results A total of 633 non-redundant proteins were identified in the serum of patients with ESCC, of which 59 and 10 proteins displayed a more than 1.5-fold increase or decrease compared with healthy controls. Verification was performed for six candidate biomarkers, including S100A8/A9, SAA1, ENO1, TPI1 and PGAM1. Receiver operating characteristics (ROC) curve plotting showed the high diagnostic sensitivity and specificity of these six protein molecules as a biomarker panel: the area under characteristic curve (AUC) is up to 0.945. Differentially expressed proteins were subjected to functional enrichment analysis, which revealed the dysregulation of signaling pathways mainly involved in glycolysis, TLR4, HIF-1α, Cori cycle, TCA cycle, folate metabolism, and platelet degranulation. The latter finding was all the more noteworthy as a strong positive correlation was discovered between activated glycolysis and TLR4 pathways and unfavorable clinicopathological TNM stages in ESCC. Conclusions Our findings propose a potential serum biomarker panel for the early detection and diagnosis of ESCC, which could potentially broaden insights into the characteristics of ESCC from the proteomic perspective. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09357-x.
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Affiliation(s)
- Wenhu Liu
- School of Pharmacy, School of Basic Medical Sciences & Forensic Medical, North Sichuan Medical College, Nanchong, China
| | - Qiang Wang
- Department of Clinical Laboratory, Translational Medicine Research Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jinxia Chang
- School of Pharmacy, School of Basic Medical Sciences & Forensic Medical, North Sichuan Medical College, Nanchong, China
| | - Anup Bhetuwal
- Sichuan Key Laboratory of Medical Imaging, North Sichuan Medical College, Nanchong, China
| | - Nisha Bhattarai
- Department of Neurology, North Sichuan Medical College, Nanchong, China
| | - Fan Zhang
- School of Pharmacy, School of Basic Medical Sciences & Forensic Medical, North Sichuan Medical College, Nanchong, China.
| | - Jiancai Tang
- School of Pharmacy, School of Basic Medical Sciences & Forensic Medical, North Sichuan Medical College, Nanchong, China.
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Sakaguchi Y, Kinumi T, Takatsu A. A Dual Functional-Group Derivatization Liquid Chromatography–Tandem Mass Spectrometry Method: Application for Quantification of Human Insulin. Chromatographia 2022. [DOI: 10.1007/s10337-022-04136-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Cardozo KHM, Lebkuchen A, Okai GG, Schuch RA, Viana LG, Olive AN, Lazari CDS, Fraga AM, Granato CFH, Pintão MCT, Carvalho VM. Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun 2020; 11:6201. [PMID: 33273458 PMCID: PMC7713649 DOI: 10.1038/s41467-020-19925-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.
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Affiliation(s)
| | - Adriana Lebkuchen
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | | | - Luciana Godoy Viana
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | - Aline Nogueira Olive
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | - Ana Maria Fraga
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
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Zhang Q, Cai Z, Lin H, Han L, Yan J, Wang J, Ke P, Zhuang J, Huang X. Expression, purification and identification of isotope-labeled recombinant cystatin C protein in Escheichia coli intended for absolute quantification using isotope dilution mass spectrometry. Protein Expr Purif 2020; 178:105785. [PMID: 33152458 DOI: 10.1016/j.pep.2020.105785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 10/23/2022]
Abstract
Isotope-labeled proteins are expected to be used as internal standard proteins in the field of protein quantification by isotope dilution mass spectrometry (ID/MS). To achieve the absolute quantification of Cystatin C (Cys C) based on ID/MS, we aims to obtain 15N isotope-labeled recombinant Cys C (15N-Cys C) protein. Firstly, the Cys C gene was optimized based on the preferred codons of Escherichia coli, and inserted into the pET-28a(+) expression plasmid. Then, the plasmid was transformed into TOP10 and BL21 strains, and 15N-Cys C was expressed in M9 medium using 15N as the only nitrogen source. 15N-Cys C was detected by SDS-PAGE, protein immunoblotting and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The characteristic peptides obtained from 15N-Cys C were analyzed by a Q Exactive Plus MS system. Results showed that 53.06% of the codons were optimized. The codon adaptation index of the Cys C genes increased from 0.31 to 0.95, and the GC content was adjusted from 64.85% to 54.88%. The purity of 15N-Cys C was higher than 95%. MALDI-TOF MS analysis showed that the m/z of 15N-Cys C had changed from 13 449 to 14 850. The characteristic peptides showed that 619.79 m/z (M+2H)2+ was the parent ion of 15N-Cys C and that the secondary ions of 15N-labeled peptides from y+5 to y+9 were 616.27 m/z, 716.33 m/z, 788.39 m/z, 936.43 m/z, and 1052.46 m/z, respectively. In conclusion, we successfully expressed, purified and identified of 15N-Cys C protein in Escheichia coli intended for absolute quantification using ID/MS.
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Affiliation(s)
- Qiaoxuan Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Zhiliang Cai
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Haibiao Lin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liqiao Han
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jun Yan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianbing Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junhua Zhuang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Xianzhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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Ji H, Xu L, Su J, Shen L, Wang H, Wang J, Wang F, Ju S. Absolute quantification of urinary neutrophil gelatinase-associated lipocalin by ultra-high-performance liquid chromatography/tandem mass spectrometry and the diagnostic efficacy of acute kidney injury. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8637. [PMID: 31659853 DOI: 10.1002/rcm.8637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/27/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE To establish an absolute quantification method for neutrophil gelatinase-associated lipocalin (NGAL) by ultra-high-performance liquid chromatography tandem positive ion electrospray ionization mass spectrometry (UHPLC/MS/MS) and evaluate its diagnostic efficacy for acute kidney injury (AKI). METHODS Three target peptides of NGA were prescreened by Skyline software, and two of them could be detected in tryptic peptides of NGAL recombinant protein and human urinary NGAL (uNGAL). Peptide (WYVVGLAGNAILR) was then selected as surrogate peptide. The corresponding isotope-labeled peptide as the internal standard was next synthesized. Quantification of uNGAL was based on equations of linear regression, and method validation was then conducted. The diagnostic efficacy of uNGAL for AKI was also evaluated using receiver operating characteristic curve (ROC) analysis. Lastly, the UHPLC/MS/MS and the particle-enhanced turbidimetric immunoassay (PETIA) methods for uNGAL quantification were compared. RESULTS For the y9 and y10 product ions, the linear regression equations were y = 2.5519x-4.6955 (R2 = 0.994, P<.01) and y = 2.4619x-4.3 (R2 =0.993, P<.01), respectively, and both of the linear ranges were from 0.5 to 15 mg/L. The limits of detection and quantification were 0.037 mg/L and 0.081 mg/L, respectively. The recoveries were from 97.32% to 107.28% at different uNGAL levels, and the within- and between-day CVs for uNGAL quantification were from 0.22% to 7.65% and from 0.66% to 5.97%, respectively. The carryover rates of uNGAL were in the range of 0.70%-0.99%. The area under the ROC curve (AUC) of uNGAL was 0.96 (P<0.01), and the sensitivity and specificity of uNGAL for AKI diagnosis were 90.0% and 92.5%, respectively. In addition, the UHPLC/MS/MS and PETIA methods showed good agreement for uNGAL quantification (y = 0.7112x-0.0139, P = 0.34). CONCLUSIONS The UHPLC/MS/MS method for uNGAL quantification has a wide linear range, high sensitivity, precision, and recovery, and low carryover rates, and uNGAL detected by this method had high sensitivity and specificity for AKI diagnosis.
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Affiliation(s)
- Huoyan Ji
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong City, Jiangsu Province, China
| | - Lili Xu
- Department of Laboratory Medicine, Nantong Maternal and Child Health Hospital, Nantong City, Jiangsu Province, China
| | - Jianyou Su
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong City, Jiangsu Province, China
| | - Lei Shen
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong City, Jiangsu Province, China
| | - Huimin Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong City, Jiangsu Province, China
| | - Jianxin Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong City, Jiangsu Province, China
| | - Feng Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong City, Jiangsu Province, China
| | - Shaoqin Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong City, Jiangsu Province, China
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8
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Chen Q, Jiang Y, Ren Y, Ying M, Lu B. Peptide Selection for Accurate Targeted Protein Quantification via a Dimethylation High-Resolution Mass Spectrum Strategy with a Peptide Release Kinetic Model. ACS OMEGA 2020; 5:3809-3819. [PMID: 32149207 PMCID: PMC7057324 DOI: 10.1021/acsomega.9b02002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
A crucial step in accurate targeted protein quantification using targeted proteomics is to determine optimal proteotypic peptides representing targeted proteins. In this study, a workflow of peptide selection to determine proteotypic peptides using a dimethylation high-resolution mass spectrum strategy with a peptide release kinetic model was investigated and applied in peptide selection of bovine serum albumin. After specificity, digestibility, recovery, and stability evaluation of tryptic peptides in bovine serum albumin, the optimal proteotypic peptide was selected as LVNELTEFAK. The quantification method using LVNELTEFAK gave a linear range of 1-100 ppm with the coefficient greater than 0.9990, and the detection limit of bovine serum albumin in milk was 0.78 mg/kg. Compared with the proteotypic peptides selected by Skyline, the method showed a better performance in method validation. The workflow exhibited high comprehensiveness and efficiency in peptide selection, facilitating accurate targeted protein quantification in the food matrix, which lack protein standards.
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Affiliation(s)
- Qi Chen
- National
Engineering Laboratory of Intelligent Food Technology and Equipment,
Key Laboratory for Agro-Products Postharvest Handling of Ministry
of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation
of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food
Processing, Fuli Institute of Food Science, College of Biosystems
Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo
Research Institute, Zhejiang University, Ningbo 315100, China
| | - Yirong Jiang
- National
Engineering Laboratory of Intelligent Food Technology and Equipment,
Key Laboratory for Agro-Products Postharvest Handling of Ministry
of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation
of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food
Processing, Fuli Institute of Food Science, College of Biosystems
Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo
Research Institute, Zhejiang University, Ningbo 315100, China
| | - Yiping Ren
- Yangtze
Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Meirong Ying
- Zhejiang
Grain and Oil Product Quality Inspection Center, Hangzhou 310012, China
| | - Baiyi Lu
- National
Engineering Laboratory of Intelligent Food Technology and Equipment,
Key Laboratory for Agro-Products Postharvest Handling of Ministry
of Agriculture, Key Laboratory for Agro-Products Nutritional Evaluation
of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food
Processing, Fuli Institute of Food Science, College of Biosystems
Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo
Research Institute, Zhejiang University, Ningbo 315100, China
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9
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Kumar AR, Shanmugasundaram KB, Li J, Zhang Z, Ibn Sina AA, Wuethrich A, Trau M. Ultrasensitive melanoma biomarker detection using a microchip SERS immunoassay with anisotropic Au–Ag alloy nanoboxes. RSC Adv 2020; 10:28778-28785. [PMID: 35520058 PMCID: PMC9055796 DOI: 10.1039/d0ra05032f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022] Open
Abstract
The detection of circulating biomarkers in liquid biopsies has the potential to provide a non-invasive route for earlier cancer diagnosis and treatment management. Melanoma chondroitin sulfate proteoglycan (MCSP) is a membrane protein characteristic for melanoma cell migration and tissue invasion with its soluble form (sMCSP) serving as a potential promising diagnostic surrogate. However, at the initial disease stage, the detection of sMCSP is challenging because of its low abundance and the required high specificity to analyze sMCSP in complex bodily fluids. Herein, we report a highly sensitive and high-throughput microchip that enables Surface Enhanced Raman Spectroscopy (SERS) immunoassay for parallel detection of up to 28 samples. Key to assay speed and sensitivity is the stimulation of an alternating current-induced nanofluidic mixing that improves target-sensor collision and displacement of non-specific molecules. Anisotropic Au–Ag alloy nanoboxes (NB's) with strong plasmonic hot spots provide single SERS particle sensitivity that enables ultrasensitive sMCSP detection of as low as 0.79 pM (200 pg ml−1). As a proof of concept study, we investigate the assay performance in simulated melanoma patient samples. The detection of circulating biomarkers in liquid biopsies has the potential to provide a non-invasive route for earlier cancer diagnosis and treatment management.![]()
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Affiliation(s)
- Aswin Raj Kumar
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Karthik Balaji Shanmugasundaram
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Junrong Li
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Zhen Zhang
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Abu Ali Ibn Sina
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Alain Wuethrich
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
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Quantitative mass spectrometry-based proteomics in the era of model-informed drug development: Applications in translational pharmacology and recommendations for best practice. Pharmacol Ther 2019; 203:107397. [DOI: 10.1016/j.pharmthera.2019.107397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/29/2019] [Indexed: 02/08/2023]
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KhalKhal E, Rezaei-Tavirani M, Rostamii-Nejad M. Pharmaceutical Advances and Proteomics Researches. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2019; 18:51-67. [PMID: 32802089 PMCID: PMC7393046 DOI: 10.22037/ijpr.2020.112440.13758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Proteomics enables understanding the composition, structure, function and interactions of the entire protein complement of a cell, a tissue, or an organism under exactly defined conditions. Some factors such as stress or drug effects will change the protein pattern and cause the present or absence of a protein or gradual variation in abundances. The aim of this study is to explore relationship between proteomics application and drug discovery. "proteomics", "Application", and "pharmacology were the main keywords that were searched in PubMed (PubMed Central), Web of Science, and Google Scholar. The titles that were stablished by 2019, were studied and after study of the appreciated abstracts, the full texts of the 118 favor documents were extracted. Changes in the proteome provide a snapshot of the cell activities and physiological processes. Proteomics shows the observed protein changes to the causal effects and generate a complete three-dimensional map of the cell indicating their exact location. Proteomics is used in different biological fields and is applied in medicine, agriculture, food microbiology, industry, and pharmacy and drug discovery. Biomarker discovery, follow up of drug effect on the patients, and in vitro and in vivo proteomic investigation about the drug treated subjects implies close relationship between proteomics advances and application and drug discovery and development. This review overviews and summarizes the applications of proteomics especially in pharmacology and drug discovery.
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Affiliation(s)
- Ensieh KhalKhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Rostamii-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Pietrowska M, Wlosowicz A, Gawin M, Widlak P. MS-Based Proteomic Analysis of Serum and Plasma: Problem of High Abundant Components and Lights and Shadows of Albumin Removal. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:57-76. [PMID: 31236839 DOI: 10.1007/978-3-030-12298-0_3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Blood serum or plasma proteome is a gold mine of disease biomarkers. However, complexity and a huge dynamic range of their components, combined with multiple mechanisms of degradation and posttranslational modifications, further complicated by the presence of lipids, salts, and other metabolites, represent a real challenge for analytical sensitivity, resolution, and reproducibility. This problem exists particularly in the case of potential disease-specific markers, most typically represented by low-abundant proteins (LAPs), whose detection is usually impaired by the dominance of albumins, immunoglobulins, and other high-abundant serum/plasma proteins (HAPs). Hence, analysis of biomarker candidates in serum/plasma samples frequently requires separation of their components, usually including depletion of albumin in a fraction of interest. Such "preprocessing" of serum/plasma specimens is critical in proteomic analysis based on mass spectrometry. This approach is very potent; nevertheless a wide range of protein concentrations in serum/plasma represents a particular challenge, since high-abundant proteins (mostly albumin) dominate in a sample subjected to mass spectrometry and suppress peptide ions originating from low-abundant proteins, thus limiting probability and reliability of their detection. An emerging approach in serum-/plasma-based biomarker-oriented studies is the proteome component of exosomes - nanovesicles secreted by cells and involved in multiple aspects of intercellular communication. However, the presence of albumin, frequent contaminant of exosomes isolated from human serum/plasma, represents a real challenge also in this type of study. A similar problem is encountered in proteomic studies based on exosomes obtained in in vitro experiments where culture media are normally supplemented with fetal bovine serum containing growth factors and hormones. In this case exosomes are frequently contaminated with bovine serum albumin and other bovine serum proteins which should be removed before proteomic analysis of exosome cargo.
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Affiliation(s)
- Monika Pietrowska
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Agata Wlosowicz
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Marta Gawin
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Piotr Widlak
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland.
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Valdés A, Lewitt M, Wiss E, Ramström M, Strage EM. Development of a Parallel Reaction Monitoring-MS Method To Quantify IGF Proteins in Dogs and a Case of Nonislet Cell Tumor Hypoglycemia. J Proteome Res 2018; 18:18-29. [PMID: 30376339 DOI: 10.1021/acs.jproteome.8b00259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Nonislet-cell tumor hypoglycemia (NICTH) is a rare paraneoplastic phenomenon well described in dogs and humans. Tumors associated with NICTH secrete incompletely processed forms of insulin-like growth factor-II (IGF-II), commonly named big IGF-II. These forms have increased bioavailability and interact with the insulin and IGF-I receptor causing hypoglycemia and growth-promoting effects. Immunoassays designed for human samples have been used to measure canine IGF-I and -II, but they possess some limitations. In addition, there are no validated methods for measurement of big IGF-II in dogs. In the present study, a targeted parallel reaction monitoring MS-based method previously developed for cats has been optimized and applied to simultaneously quantify the serum levels of IGF-I, IGF-II, and IGFBP-3, and for the first time, the levels of big IGF-II in dogs. This method allows the absolute quantification of IGF proteins using a mixture of QPrEST proteins previously designed for humans. The method possesses good linearity and repeatability and has been used to evaluate the IGF-system in a dog with NICTH syndrome. In this dog, the levels of big IGF-II decreased by 80% and the levels of IGF-I and IGFBP-3 increased approximately 20- and 4-times, respectively, after removal of the tumor.
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Affiliation(s)
- Alberto Valdés
- Department of Chemistry-BMC, Analytical Chemistry , Uppsala University , 75123 Uppsala , Sweden
| | - Moira Lewitt
- School of Health and Life Sciences , University of the West of Scotland , PA1 2BE Paisley , United Kingdom
| | - Erica Wiss
- Albano Animal Hospital , 182 36 Stockholm , Sweden
| | - Margareta Ramström
- Department of Chemistry-BMC, Analytical Chemistry , Uppsala University , 75123 Uppsala , Sweden
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14
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Schneck NA, Phinney KW, Lee SB, Lowenthal MS. Quantification of cardiac troponin I in human plasma by immunoaffinity enrichment and targeted mass spectrometry. Anal Bioanal Chem 2018; 410:2805-2813. [PMID: 29492621 DOI: 10.1007/s00216-018-0960-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/05/2018] [Accepted: 02/12/2018] [Indexed: 01/17/2023]
Abstract
Quantification of cardiac troponin I (cTnI), a protein biomarker used for diagnosing myocardial infarction, has been achieved in native patient plasma based on an immunoaffinity enrichment strategy and isotope dilution (ID) liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. The key steps in the workflow involved isolating cTnI from plasma using anti-cTnI antibody coupled to magnetic nanoparticles, followed by an enzymatic digestion with trypsin. Three tryptic peptides from cTnI were monitored and used for quantification by ID-LC-MS/MS via multiple reaction monitoring (MRM). Measurements were performed using a matrix-matched calibration system. NIST SRM 2921 Human Cardiac Troponin Complex acted as the calibrant and a full-length isotopically labeled protein analog of cTnI was used as an internal standard. The method was successfully demonstrated on five patient plasma samples, with cTnI concentrations measuring between 4.86 μg/L and 11.3 μg/L (signifying moderate myocardial infarctions). LC-MS/MS measurement precision was validated by three unique peptides from cTnI and two MRM transitions per peptide. Relative standard deviation (CV) from the five plasma samples was determined to be ≤14.3%. This study has demonstrated that quantification of cTnI in native plasma from myocardial infarction patients can be achieved based on an ID-LC-MS/MS method. The development of an ID-LC-MS/MS method for cTnI in plasma is a first step for future certification of matrix-based reference materials, which may be used to help harmonize discordant cTnI clinical assays. Graphical abstract A schematic of the workflow for measuring cardiac troponin I (cTnI), a low-abundant protein biomarker used for diagnosing myocardial infarction, in human plasma by isotope-dilution LC-MS/MS analysis.
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Affiliation(s)
- Nicole A Schneck
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8314, Gaithersburg, MD, 20899, USA
| | - Karen W Phinney
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8314, Gaithersburg, MD, 20899, USA
| | - Sang Bok Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
| | - Mark S Lowenthal
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8314, Gaithersburg, MD, 20899, USA.
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15
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Olkowicz M, Jablonska P, Rogowski J, Smolenski RT. Simultaneous accurate quantification of HO-1, CD39, and CD73 in human calcified aortic valves using multiple enzyme digestion - filter aided sample pretreatment (MED-FASP) method and targeted proteomics. Talanta 2018; 182:492-499. [PMID: 29501184 DOI: 10.1016/j.talanta.2018.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/05/2023]
Abstract
Several proteins such as membrane-associated ectonucleotidases: ecto-5'-nucleotidase (E5NT/CD73) and ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1/CD39), and intracellular heme oxygenase-1 (HO-1) may contribute to protection from inflammation-related diseases such as calcific aortic valve stenosis (CAS). Accurate quantification of these proteins could contribute to better understanding of the disease mechanisms and identification of biomarkers. This report presents development and validation of quantification method for E5NT/CD73, ENTPD1/CD39 and HO-1. The multiplexed targeted proteomic assay involved antibody-free, multiple-enzyme digestion, filter-assisted sample preparation (MED-FASP) strategy and a nanoflow liquid chromatography/mass spectrometry under multiple reaction monitoring mode (LC-MRM/MS). The method developed presented high sensitivity (LLOQ of 5 pg/mL for each of the analytes) and accuracy that ranged from 92.0% to 107.0%, and was successfully applied for the absolute quantification of HO-1, CD39 and CD73 proteins in homogenates of human calcified and non-calcified valves. The absolute CD39 and CD73 concentrations were lower in calcified aortic valves (as compared to non-stenotic ones) and were found to be: 1.16 ± 0.39 vs. 3.15 ± 0.37 pmol/mg protein and 1.94 ± 0.21 vs. 2.39 ± 0.39 pmol/mg protein, respectively, while the quantity of HO-1 was elevated in calcified valves (10.72 ± 1.18 vs. 4.28 ± 0.42 amol/mg protein). These results were consistent but more reproducible as compared to immunoassays. In conclusion, multiplexed quantification of HO-1, CD39 and CD73 proteins by LC-MRM/MS works well in challenging human tissues such as aortic valves. This analysis confirmed the relevance of these proteins in pathogenesis of CAS and could be extended to other biomedical investigations.
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Affiliation(s)
- Mariola Olkowicz
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego St., 60-627 Poznan, Poland.
| | - Patrycja Jablonska
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland
| | - Jan Rogowski
- Department of Cardiac and Vascular Surgery, Medical University of Gdansk, 7 Debinki St., 80-211 Gdansk, Poland
| | - Ryszard T Smolenski
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland
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16
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Hibbert SA, Ozols M, Griffiths CEM, Watson REB, Bell M, Sherratt MJ. Defining tissue proteomes by systematic literature review. Sci Rep 2018; 8:546. [PMID: 29323144 PMCID: PMC5765030 DOI: 10.1038/s41598-017-18699-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/14/2017] [Indexed: 12/24/2022] Open
Abstract
Defining protein composition is a key step in understanding the function of both healthy and diseased biological systems. There is currently little consensus between existing published proteomes in tissues such as the aorta, cartilage and organs such as skin. Lack of agreement as to both the number and identity of proteins may be due to issues in protein extraction, sensitivity/specificity of detection and the use of disparate tissue/cell sources. Here, we developed a method combining bioinformatics and systematic review to screen >32M articles from the Web of Science for evidence of proteins in healthy human skin. The resulting Manchester Proteome (www.manchesterproteome.manchester.ac.uk) collates existing evidence which characterises 2,948 skin proteins, 437 unique to our database and 2011 evidenced by both mass spectrometry and immune-based techniques. This approach circumvents the limitations of individual proteomics studies and can be applied to other species, organs, cells or disease-states. Accurate tissue proteomes will aid development of engineered constructs and offer insight into disease treatments by highlighting differences in proteomic composition.
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Affiliation(s)
- Sarah A Hibbert
- Division of Cell Matrix Biology & Regenerative Medicine, The University of Manchester, Manchester, UK.
| | - Matiss Ozols
- Division of Cell Matrix Biology & Regenerative Medicine, The University of Manchester, Manchester, UK
| | - Christopher E M Griffiths
- Centre for Dermatology Research, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachel E B Watson
- Centre for Dermatology Research, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Mike Bell
- Walgreens Boots Alliance, Thane Road, Nottingham, UK
| | - Michael J Sherratt
- Division of Cell Matrix Biology & Regenerative Medicine, The University of Manchester, Manchester, UK.
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17
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Lindsey ML, Jung M, Hall ME, DeLeon-Pennell KY. Proteomic analysis of the cardiac extracellular matrix: clinical research applications. Expert Rev Proteomics 2018; 15:105-112. [PMID: 29285949 DOI: 10.1080/14789450.2018.1421947] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The cardiac extracellular matrix (ECM) provides anatomical, biochemical, and physiological support to the left ventricle. ECM proteins are difficult to detect using unbiased proteomic approaches due to solubility issues and a relatively low abundance compared to cytoplasmic and mitochondrial proteins present in highly prevalent cardiomyocytes. Areas covered: Proteomic capabilities have dramatically improved over the past 20 years, due to enhanced sample preparation protocols and increased capabilities in mass spectrometry (MS), database searching, and bioinformatics analysis. This review summarizes technological advancements made in proteomic applications that make ECM proteomics highly feasible. Expert commentary: Proteomic analysis of the ECM provides an important contribution to our understanding of the molecular and cellular processes associated with cardiovascular disease. Using results generated from proteomics approaches in basic science applications and integrating proteomics templates into clinical research protocols will aid in efforts to personalize medicine.
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Affiliation(s)
- Merry L Lindsey
- a Research Service , G.V. (Sonny) Montgomery Veterans Affairs Medical Center , Jackson , MS , USA.,b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
| | - Mira Jung
- b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
| | - Michael E Hall
- b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA.,c Division of Cardiology , University of Mississippi Medical Center , Jackson , MS , USA
| | - Kristine Y DeLeon-Pennell
- a Research Service , G.V. (Sonny) Montgomery Veterans Affairs Medical Center , Jackson , MS , USA.,b Mississippi Center for Heart Research, Department of Physiology and Biophysics , University of Mississippi Medical Center , Jackson , MS , USA
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18
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Dridi N, Giremus A, Giovannelli JF, Truntzer C, Hadzagic M, Charrier JP, Gerfault L, Ducoroy P, Lacroix B, Grangeat P, Roy P. Bayesian inference for biomarker discovery in proteomics: an analytic solution. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2017; 2017:9. [PMID: 28710702 PMCID: PMC5511129 DOI: 10.1186/s13637-017-0062-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 06/21/2017] [Indexed: 12/02/2022]
Abstract
This paper addresses the question of biomarker discovery in proteomics. Given clinical data regarding a list of proteins for a set of individuals, the tackled problem is to extract a short subset of proteins the concentrations of which are an indicator of the biological status (healthy or pathological). In this paper, it is formulated as a specific instance of variable selection. The originality is that the proteins are not investigated one after the other but the best partition between discriminant and non-discriminant proteins is directly sought. In this way, correlations between the proteins are intrinsically taken into account in the decision. The developed strategy is derived in a Bayesian setting, and the decision is optimal in the sense that it minimizes a global mean error. It is finally based on the posterior probabilities of the partitions. The main difficulty is to calculate these probabilities since they are based on the so-called evidence that require marginalization of all the unknown model parameters. Two models are presented that relate the status to the protein concentrations, depending whether the latter are biomarkers or not. The first model accounts for biological variabilities by assuming that the concentrations are Gaussian distributed with a mean and a covariance matrix that depend on the status only for the biomarkers. The second one is an extension that also takes into account the technical variabilities that may significantly impact the observed concentrations. The main contributions of the paper are: (1) a new Bayesian formulation of the biomarker selection problem, (2) the closed-form expression of the posterior probabilities in the noiseless case, and (3) a suitable approximated solution in the noisy case. The methods are numerically assessed and compared to the state-of-the-art methods (t test, LASSO, Battacharyya distance, FOHSIC) on synthetic and real data from proteins quantified in human serum by mass spectrometry in selected reaction monitoring mode.
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Affiliation(s)
- Noura Dridi
- IMS (Univ. Bordeaux, CNRS, BINP), Talence, 33400 France
- National Engineering School of Gabes (ENIG), University of Gabes, Gabes, Tunisia
| | | | | | - Caroline Truntzer
- CLIPP, Pôle de Recherche Université de Bourgogne, Dijon, 21000 France
| | - Melita Hadzagic
- IMS (Univ. Bordeaux, CNRS, BINP), Talence, 33400 France
- NATO STO Centre for Maritime Research and Experimentation, La Spezia, 19126 Italy
| | | | - Laurent Gerfault
- Univ. Grenoble Alpes, Grenoble, F-38000 France
- CEA, LETI, MINATEC Campus, Grenoble, F-38054 France
| | - Patrick Ducoroy
- CLIPP, Pôle de Recherche Université de Bourgogne, Dijon, 21000 France
| | - Bruno Lacroix
- Technology Research Department, Innovation Unit, bioMérieux SA, Marcy l’Étoile, France
| | - Pierre Grangeat
- Univ. Grenoble Alpes, Grenoble, F-38000 France
- CEA, LETI, MINATEC Campus, Grenoble, F-38054 France
| | - Pascal Roy
- Service de Biostatistique - Bioinformatique, Hospices Civils de Lyon, Lyon, France
- CNRS UMR 5558, LBBE, Équipe Biostatistique Santé, Villeurbanne, France
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Pôle Rhône-Alpes de Bioinformatique, Université Claude Bernard - Lyon 1, Villeurbanne, 69622 France
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19
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Absolute Quantification of Middle- to High-Abundant Plasma Proteins via Targeted Proteomics. Methods Mol Biol 2017. [PMID: 28674901 DOI: 10.1007/978-1-4939-7057-5_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The increasing number of peptide and protein biomarker candidates requires expeditious and reliable quantification strategies. The utilization of liquid chromatography coupled to quadrupole tandem mass spectrometry (LC-MS/MS) for the absolute quantitation of plasma proteins and peptides facilitates the multiplexed verification of tens to hundreds of biomarkers from smallest sample quantities. Targeted proteomics assays derived from bottom-up proteomics principles rely on the identification and analysis of proteotypic peptides formed in an enzymatic digestion of the target protein. This protocol proposes a procedure for the establishment of a targeted absolute quantitation method for middle- to high-abundant plasma proteins waiving depletion or enrichment steps. Essential topics as proteotypic peptide identification and LC-MS/MS method development as well as sample preparation and calibration strategies are described in detail.
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20
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Mokou M, Lygirou V, Vlahou A, Mischak H. Proteomics in cardiovascular disease: recent progress and clinical implication and implementation. Expert Rev Proteomics 2017; 14:117-136. [DOI: 10.1080/14789450.2017.1274653] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marika Mokou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Harald Mischak
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
- Mosaiques Diagnostics, Hannover, Germany
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21
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Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH. Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600097] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/14/2016] [Accepted: 09/28/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Sarah A. Michaud
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Armando Jardim
- Institute of Parasitology; McGill University; Montreal QC Canada
| | - Nicholas J. Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Suping Zhang
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Center for Proteomics and Metabolomics; Leiden University Medical Center; ZA Leiden Netherlands
| | - Andrea L. Palmer
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Darryl B. Hardie
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Andre M. LeBlanc
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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22
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Grebe SK, Singh RJ. Clinical peptide and protein quantification by mass spectrometry (MS). Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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23
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Lesur A, Gallien S, Domon B. Hyphenation of fast liquid chromatography with high-resolution mass spectrometry for quantitative proteomics analyses. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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25
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Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep 2016; 6:24799. [PMID: 27142790 PMCID: PMC4855174 DOI: 10.1038/srep24799] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/30/2016] [Indexed: 12/29/2022] Open
Abstract
The central dogma of molecular biology describes the translation of genetic information from mRNA to protein, but does not specify the quantitation or timing of this process across the genome. We have analyzed protein and gene expression in a diverse set of human tissues. To study concordance and discordance of gene and protein expression, we integrated mass spectrometry data from the Human Proteome Map project and RNA-Seq measurements from the Genotype-Tissue Expression project. We analyzed 16,561 genes and the corresponding proteins in 14 tissue types across nearly 200 samples. A comprehensive tissue- and gene-specific analysis revealed that across the 14 tissues, correlation between mRNA and protein expression was positive and ranged from 0.36 to 0.5. We also identified 1,012 genes whose RNA and protein expression was correlated across all the tissues and examined genes and proteins that were concordantly and discordantly expressed for each tissue of interest. We extended our analysis to look for genes and proteins that were differentially correlated in cancer compared to normal tissues, showing higher levels of correlation in normal tissues. Finally, we explored the implications of these findings in the context of biomarker and drug target discovery.
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26
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Sabbagh B, Mindt S, Neumaier M, Findeisen P. Clinical applications of MS-based protein quantification. Proteomics Clin Appl 2016; 10:323-45. [DOI: 10.1002/prca.201500116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/18/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Bassel Sabbagh
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Sonani Mindt
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
- MVZ Labor Dr. Limbach und Kollegen; Heidelberg Germany
- Working Group Proteomics of the German United Society for Clinical Chemistry and Laboratory Medicine e.V. (DGKL); Bonn Germany
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27
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Josić D, Andjelković U. The Role of Proteomics in Personalized Medicine. Per Med 2016. [DOI: 10.1007/978-3-319-39349-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Rauniyar N. Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry. Int J Mol Sci 2015; 16:28566-81. [PMID: 26633379 PMCID: PMC4691067 DOI: 10.3390/ijms161226120] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022] Open
Abstract
The parallel reaction monitoring (PRM) assay has emerged as an alternative method of targeted quantification. The PRM assay is performed in a high resolution and high mass accuracy mode on a mass spectrometer. This review presents the features that make PRM a highly specific and selective method for targeted quantification using quadrupole-Orbitrap hybrid instruments. In addition, this review discusses the label-based and label-free methods of quantification that can be performed with the targeted approach.
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Affiliation(s)
- Navin Rauniyar
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, 300 George Street, New Haven, CT 06511, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
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29
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Hu LZ, Zhang WP, Zhou MT, Han QQ, Gao XL, Zeng HL, Guo L. Analysis of Salmonella PhoP/PhoQ regulation by dimethyl-SRM-based quantitative proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:20-8. [PMID: 26472331 DOI: 10.1016/j.bbapap.2015.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/29/2015] [Accepted: 10/09/2015] [Indexed: 02/01/2023]
Abstract
SRM (selected reaction monitoring), a tandem mass spectrometry-based method characterized by high repeatability and accuracy, is an effective tool for the quantification of predetermined proteins. In this study, we built a time-scheduled dimethyl-SRM method that can provide the precise relative quantification of 92 proteins in one run. By applying this method to the Salmonella PhoP/PhoQ two-component system, we found that the expression of selected PhoP/PhoQ-activated proteins in response to Mg(2+) concentrations could be divided into two distinct patterns. For the time-course SRM experiment, we found that the dynamics of the selected PhoP/PhoQ-activated proteins could be divided into three distinct patterns, providing a new clue regarding PhoP/PhoQ activation and regulation. Moreover, the results for iron homeostasis proteins in response to Mg(2+) concentrations revealed that the PhoP/PhoQ two-component system may serve as a repressor for iron uptake proteins. And ribosomal protein levels clearly showed a response to different Mg(2+) concentrations and to time.
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Affiliation(s)
- Li-Zhi Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wei-Ping Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mao-Tian Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiang-Qiang Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao-Li Gao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hao-Long Zeng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.
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30
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Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 2015; 15:3193-208. [PMID: 26097198 PMCID: PMC4758406 DOI: 10.1002/pmic.201500004] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/27/2015] [Accepted: 06/09/2015] [Indexed: 01/28/2023]
Abstract
Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM-MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alex Root
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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31
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Bros P, Vialaret J, Barthelemy N, Delatour V, Gabelle A, Lehmann S, Hirtz C. Antibody-free quantification of seven tau peptides in human CSF using targeted mass spectrometry. Front Neurosci 2015; 9:302. [PMID: 26388715 PMCID: PMC4555028 DOI: 10.3389/fnins.2015.00302] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022] Open
Abstract
Tau protein concentration in cerebrospinal fluid (CSF) is currently used as a sensitive and specific biomarker for Alzheimer's disease. Its detection currently relies on ELISA but the perspective of using mass spectrometry (MS) to detect its different proteoforms represents an interesting alternative. This is however an analytical challenge because of its low concentration in the CSF, a biological fluid collected in small volume by lumbar puncture, and with a high structural heterogeneity. To overcome these issues, instead of using immunocapture as previously done, we rather relied on an original two steps pre-fractionation technique of CSF: perchloric acid (PCA) followed by micro solid phase extraction (μSPE). We could then measure seven tau trypsic peptides by Multiple Reaction Monitoring (MRM) on a triple quadrupole mass spectrometer. Quantification was performed using isotopically labeled 15N- recombinant tau protein as internal standard and validated using CSF pools with low, medium, or high tau concentrations (HTCs). Repeatability, intermediate precision, linearity, limit of quantification (LOQ), and recovery were calculated for the different peptides. This new MRM assay, which allowed for the first time CSF tau protein quantification without immunocapture, has important potential application to follow tau metabolism in both diagnostic and therapeutic research.
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Affiliation(s)
- Pauline Bros
- Laboratoire de Biochimie et de Protéomique Clinique - Institut de Médecine Régénérative et Biothérapies, Centre Hospitalier Universitaire de Montpellier Montpellier, France ; Laboratoire National de Métrologie et d'Essais (LNE) Paris, France
| | - Jérôme Vialaret
- Laboratoire de Biochimie et de Protéomique Clinique - Institut de Médecine Régénérative et Biothérapies, Centre Hospitalier Universitaire de Montpellier Montpellier, France
| | - Nicolas Barthelemy
- Laboratoire de Biochimie et de Protéomique Clinique - Institut de Médecine Régénérative et Biothérapies, Centre Hospitalier Universitaire de Montpellier Montpellier, France
| | - Vincent Delatour
- Laboratoire National de Métrologie et d'Essais (LNE) Paris, France
| | - Audrey Gabelle
- Laboratoire de Biochimie et de Protéomique Clinique - Institut de Médecine Régénérative et Biothérapies, Centre Hospitalier Universitaire de Montpellier Montpellier, France ; Centre Mémoire Ressources Recherche, Centre Hospitalier Universitaire de Montpellier, Hôpital Gui de Chauliac, Université Montpellier I Montpellier, France
| | - Sylvain Lehmann
- Laboratoire de Biochimie et de Protéomique Clinique - Institut de Médecine Régénérative et Biothérapies, Centre Hospitalier Universitaire de Montpellier Montpellier, France
| | - Christophe Hirtz
- Laboratoire de Biochimie et de Protéomique Clinique - Institut de Médecine Régénérative et Biothérapies, Centre Hospitalier Universitaire de Montpellier Montpellier, France
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32
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Mass spectrometry-based proteomics for pre-eclampsia and preterm birth. Int J Mol Sci 2015; 16:10952-85. [PMID: 26006232 PMCID: PMC4463685 DOI: 10.3390/ijms160510952] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/04/2015] [Indexed: 12/15/2022] Open
Abstract
Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered.
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33
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Butt AQ, McArdle A, Gibson DS, FitzGerald O, Pennington SR. Psoriatic Arthritis Under a Proteomic Spotlight: Application of Novel Technologies to Advance Diagnosis and Management. Curr Rheumatol Rep 2015; 17:35. [DOI: 10.1007/s11926-015-0509-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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34
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Mohammed Y, Percy AJ, Chambers AG, Borchers CH. Qualis-SIS: automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards. J Proteome Res 2015; 14:1137-46. [PMID: 25546269 DOI: 10.1021/pr5010955] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiplexed targeted quantitative proteomics typically utilizes multiple reaction monitoring and allows the optimized quantification of a large number of proteins. One challenge, however, is the large amount of data that needs to be reviewed, analyzed, and interpreted. Different vendors provide software for their instruments, which determine the recorded responses of the heavy and endogenous peptides and perform the response-curve integration. Bringing multiplexed data together and generating standard curves is often an off-line step accomplished, for example, with spreadsheet software. This can be laborious, as it requires determining the concentration levels that meet the required accuracy and precision criteria in an iterative process. We present here a computer program, Qualis-SIS, that generates standard curves from multiplexed MRM experiments and determines analyte concentrations in biological samples. Multiple level-removal algorithms and acceptance criteria for concentration levels are implemented. When used to apply the standard curve to new samples, the software flags each measurement according to its quality. From the user's perspective, the data processing is instantaneous due to the reactivity paradigm used, and the user can download the results of the stepwise calculations for further processing, if necessary. This allows for more consistent data analysis and can dramatically accelerate the downstream data analysis.
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Affiliation(s)
- Yassene Mohammed
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria , Vancouver Island Technology Park, #3101-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
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35
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Puangpila C, Mayadunne E, El Rassi Z. Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2011-2014. Electrophoresis 2015; 36:238-52. [PMID: 25287967 PMCID: PMC4485988 DOI: 10.1002/elps.201400434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 11/07/2022]
Abstract
This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As the previous review article, the present one is concerned with proteomic sample preparation (e.g., depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article, however, is distinguished from its earlier version by expanding on capturing/enriching subphosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid-2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field.
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Affiliation(s)
- Chanida Puangpila
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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36
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Dittrich J, Becker S, Hecht M, Ceglarek U. Sample preparation strategies for targeted proteomics via proteotypic peptides in human blood using liquid chromatography tandem mass spectrometry. Proteomics Clin Appl 2014; 9:5-16. [PMID: 25418444 DOI: 10.1002/prca.201400121] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 11/07/2022]
Abstract
The simultaneous quantification of protein concentrations via proteotypic peptides in human blood by liquid chromatography coupled to quadrupole MS/MS is an important field of bioanalytical research with a high potential for routine diagnostic applications. This review summarizes currently available sample preparation procedures and trends for absolute protein quantification in blood using LC-MS/MS. It discusses approaches of transferring established qualitative protocols to a quantitative analysis regarding their reliability and reproducibility. Techniques used to enhance method sensitivity such as the depletion of high-abundant proteins or the immunoaffinity enrichment of proteins and peptides are described. Furthermore, workflows for (i) protein denaturation, (ii) disulfide bridge reduction and (iii) thiol alkylation as well as (iv) enzymatic digestion for absolute protein quantification are presented. The main focus is on the tryptic digestion as a bottleneck of protein quantification via proteotypic peptides. Conclusively, requirements for a high-throughput application are discussed.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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37
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Takemori N, Takemori A, Matsuoka K, Morishita R, Matsushita N, Aoshima M, Takeda H, Sawasaki T, Endo Y, Higashiyama S. High-throughput synthesis of stable isotope-labeled transmembrane proteins for targeted transmembrane proteomics using a wheat germ cell-free protein synthesis system. MOLECULAR BIOSYSTEMS 2014; 11:361-5. [PMID: 25431973 DOI: 10.1039/c4mb00556b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a wheat germ cell-free protein synthesis system, we developed a high-throughput method for the synthesis of stable isotope-labeled full-length transmembrane proteins as proteoliposomes to mimic the in vivo environment, and we successfully constructed an internal standard library for targeted transmembrane proteomics by using mass spectrometry.
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38
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Bundgaard L, Jacobsen S, Dyrlund TF, Sørensen MA, Harman VM, Beynon RJ, Brownridge PJ, Petersen LJ, Bendixen E. Development of a Method for Absolute Quantification of Equine Acute Phase Proteins Using Concatenated Peptide Standards and Selected Reaction Monitoring. J Proteome Res 2014; 13:5635-47. [DOI: 10.1021/pr500607s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Louise Bundgaard
- Department
of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Højbakkegaard Allé 5, Taastrup 2630, Denmark
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 10c, Aarhus 8000, Denmark
| | - Stine Jacobsen
- Department
of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Højbakkegaard Allé 5, Taastrup 2630, Denmark
| | - Thomas F. Dyrlund
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 10c, Aarhus 8000, Denmark
| | - Mette Aa. Sørensen
- Department
of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Højbakkegaard Allé 5, Taastrup 2630, Denmark
| | - Victoria M. Harman
- Protein
Function Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Robert J. Beynon
- Protein
Function Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Philip J. Brownridge
- Protein
Function Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Lars J. Petersen
- Department
of Nuclear Medicine, Clinical Cancer Research Center, Aalborg University Hospital, Hobrovej 18-22, Aalborg 9000, Denmark
- Department
of Clinical Medicine, Aalborg University Hospital, Sdr. Skovvej 11, Aalborg 9000, Denmark
| | - Emøke Bendixen
- Department
of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 10c, Aarhus 8000, Denmark
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39
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Gianazza E, Tremoli E, Banfi C. The selected reaction monitoring/multiple reaction monitoring-based mass spectrometry approach for the accurate quantitation of proteins: clinical applications in the cardiovascular diseases. Expert Rev Proteomics 2014; 11:771-88. [PMID: 25400095 DOI: 10.1586/14789450.2014.947966] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Selected reaction monitoring, also known as multiple reaction monitoring, is a powerful targeted mass spectrometry approach for a confident quantitation of proteins/peptides in complex biological samples. In recent years, its optimization and application have become pivotal and of great interest in clinical research to derive useful outcomes for patient care. Thus, selected reaction monitoring/multiple reaction monitoring is now used as a highly sensitive and selective method for the evaluation of protein abundances and biomarker verification with potential applications in medical screening. This review describes technical aspects for the development of a robust multiplex assay and discussing its recent applications in cardiovascular proteomics: verification of promising disease candidates to select only the highest quality peptides/proteins for a preclinical validation, as well as quantitation of protein isoforms and post-translational modifications.
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Affiliation(s)
- Erica Gianazza
- Laboratory of Cell Biology and Biochemistry of Atherothrombosis, Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Via Parea 4, 20138 Milan, Italy
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40
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Shen X, Young R, Canty JM, Qu J. Quantitative proteomics in cardiovascular research: global and targeted strategies. Proteomics Clin Appl 2014; 8:488-505. [PMID: 24920501 DOI: 10.1002/prca.201400014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/02/2014] [Accepted: 06/06/2014] [Indexed: 11/05/2022]
Abstract
Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here, we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation.
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Affiliation(s)
- Xiaomeng Shen
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
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41
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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42
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Simon R, Passeron S, Lemoine J, Salvador A. Hydrophilic interaction liquid chromatography as second dimension in multidimensional chromatography with an anionic trapping strategy: application to prostate-specific antigen quantification. J Chromatogr A 2014; 1354:75-84. [PMID: 24931446 DOI: 10.1016/j.chroma.2014.05.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/22/2014] [Accepted: 05/24/2014] [Indexed: 12/17/2022]
Abstract
Liquid chromatography (LC) coupled with tandem mass spectrometry (MS-MS) in selected reaction monitoring mode (SRM) has become a widely used technique for the quantification of protein biomarkers in plasma and has already proven to give similar results compared to the conventional immunoassays. To improve the lack of insufficient sensitivity for quantification of low abundance protein, we propose a new two dimensional liquid chromatography (2D-LC-SRM) method for the quantitation of prostate specific antigen (PSA) in human plasma. The method centers on anion exchange cartridge between reversed-phase chromatography and hydrophilic interaction liquid chromatography (HILIC) in an on-line arrangement. The use of the anionic cartridge allows an easier online transfer of the analytes between both dimensions. Moreover, it provides an additional selectivity since the more basic peptides are not retained on this support. This setup has been applied to the quantification of prostate specific antigen (PSA) protein in plasma on a previous generation of mass spectrometer, which enabled a limit of quantification (LOQ) of 1ng/mL without any upfront immuno-depletion or intense off-line fractionation before the SRM analysis. The obtained LOQ is compatible with the required sensitivity for the clinically relevant plasma-based PSA tests.
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Affiliation(s)
- Romain Simon
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Sébastien Passeron
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Jérôme Lemoine
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Arnaud Salvador
- UMR 5280, Institut des sciences analytiques, Université de Lyon, Lyon 1, 5 Rue de la Doua, 69100 Villeurbanne, France.
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43
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Zhao C, Trudeau B, Xie H, Prostko J, Fishpaugh J, Ramsay C. Epitope mapping and targeted quantitation of the cardiac biomarker troponin by SID-MRM mass spectrometry. Proteomics 2014; 14:1311-21. [PMID: 24596168 DOI: 10.1002/pmic.201300150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 02/05/2014] [Accepted: 02/27/2014] [Indexed: 11/09/2022]
Abstract
The absolute quantitation of the targeted protein using MS provides a promising method to evaluate/verify biomarkers used in clinical diagnostics. In this study, a cardiac biomarker, troponin I (TnI), was used as a model protein for method development. The epitope peptide of TnI was characterized by epitope excision followed with LC/MS/MS method and acted as the surrogate peptide for the targeted protein quantitation. The MRM-based MS assay using a stable internal standard that improved the selectivity, specificity, and sensitivity of the protein quantitation. Also, plasma albumin depletion and affinity enrichment of TnI by anti-TnI mAb-coated microparticles reduced the sample complexity, enhanced the dynamic range, and further improved the detecting sensitivity of the targeted protein in the biological matrix. Therefore, quantitation of TnI, a low abundant protein in human plasma, has demonstrated the applicability of the targeted protein quantitation strategy through its epitope peptide determined by epitope mapping method.
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Affiliation(s)
- Cheng Zhao
- Research Analytical Chemistry, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, USA
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44
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Nouri-Nigjeh E, Zhang M, Ji T, Yu H, An B, Duan X, Balthasar J, Johnson RW, Qu J. Effects of calibration approaches on the accuracy for LC-MS targeted quantification of therapeutic protein. Anal Chem 2014; 86:3575-84. [PMID: 24611550 PMCID: PMC3982980 DOI: 10.1021/ac5001477] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
LC–MS
provides a promising alternative to ligand-binding
assays for quantification of therapeutic proteins and biomarkers.
As LC–MS methodology is based on the analysis of proteolytic
peptides, calibration approaches utilizing various calibrators and
internal standards (I.S.) have been developed. A comprehensive assessment
of the accuracy and reliability of these approaches is essential but
has yet been reported. Here we performed a well-controlled and systematic
comparative study using quantification of monoclonal-antibody in plasma
as the model system. Method development utilized a high-throughput
orthogonal-array-optimization, and two sensitive and stable signature-peptides
(SP) from different domains were selected based on extensive evaluations
in plasma matrix. With the purities of all protein/peptide standards
corrected by quantitative amino acid analysis (AAA), five calibration
approaches using stable-isotope-labeled (SIL) I.S. were thoroughly
compared, including those at peptide, extended-peptide, and protein
levels and two “hybrid” approaches (i.e., protein calibrator
with SIL-peptide or SIL-extended-peptide I.S.). These approaches were
further evaluated in parallel for a 15 time point, preclinical pharmacokinetic
study. All methods showed good precision (CV% < 20%). When examined
with protein-spiked plasma QC, peptide-level calibration exhibited
severe negative biases (−23 to −62%), highly discordant
results between the two SP (deviations of 38–56%), and misleading
pharmacokinetics assessments. Extended-peptide calibration showed
significant improvements but still with unacceptable accuracy. Conversely,
protein-level and the two hybrid calibrations achieved good quantitative
accuracy (error < 10%), concordant results by two SP (deviations
< 15%), and correct pharmacokinetic parameters. Hybrid approaches
were found to provide a cost-effective means for accurate quantification
without the costly SIL-protein. Other key findings include (i) using
two SP provides a versatile gauge for method reliability; (ii) evaluation
of peptide stability in the matrix before SP selection is critical;
and (iii) using AAA to verify purities of protein/peptide calibrators
ensures accurate quantitation. These results address fundamental calibration
issues that have not been adequately investigated in published studies
and will provide valuable guidelines for the “fit for purpose”
development of accurate LC–MS assays for therapeutic proteins
and biomarkers in biological matrices.
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Affiliation(s)
- Eslam Nouri-Nigjeh
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York , Amherst, NY 14260, United States
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Trauchessec M, Jaquinod M, Bonvalot A, Brun V, Bruley C, Ropers D, de Jong H, Garin J, Bestel-Corre G, Ferro M. Mass spectrometry-based workflow for accurate quantification of Escherichia coli enzymes: how proteomics can play a key role in metabolic engineering. Mol Cell Proteomics 2014; 13:954-68. [PMID: 24482123 DOI: 10.1074/mcp.m113.032672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metabolic engineering aims to design high performance microbial strains producing compounds of interest. This requires systems-level understanding; genome-scale models have therefore been developed to predict metabolic fluxes. However, multi-omics data including genomics, transcriptomics, fluxomics, and proteomics may be required to model the metabolism of potential cell factories. Recent technological advances to quantitative proteomics have made mass spectrometry-based quantitative assays an interesting alternative to more traditional immuno-affinity based approaches. This has improved specificity and multiplexing capabilities. In this study, we developed a quantification workflow to analyze enzymes involved in central metabolism in Escherichia coli (E. coli). This workflow combined full-length isotopically labeled standards with selected reaction monitoring analysis. First, full-length (15)N labeled standards were produced and calibrated to ensure accurate measurements. Liquid chromatography conditions were then optimized for reproducibility and multiplexing capabilities over a single 30-min liquid chromatography-MS analysis. This workflow was used to accurately quantify 22 enzymes involved in E. coli central metabolism in a wild-type reference strain and two derived strains, optimized for higher NADPH production. In combination with measurements of metabolic fluxes, proteomics data can be used to assess different levels of regulation, in particular enzyme abundance and catalytic rate. This provides information that can be used to design specific strains used in biotechnology. In addition, accurate measurement of absolute enzyme concentrations is key to the development of predictive kinetic models in the context of metabolic engineering.
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Affiliation(s)
- Mathieu Trauchessec
- Commisariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologie et Sciences pour le Vivant (iRTSV), Biologie à Grande Echelle, F-38054 Grenoble, France
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Percy AJ, Byrns S, Chambers AG, Borchers CH. Targeted quantitation of CVD-linked plasma proteins for biomarker verification and validation. Expert Rev Proteomics 2014; 10:567-78. [DOI: 10.1586/14789450.2013.856763] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Villanueva J, Carrascal M, Abian J. Isotope dilution mass spectrometry for absolute quantification in proteomics: Concepts and strategies. J Proteomics 2014; 96:184-99. [DOI: 10.1016/j.jprot.2013.11.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/25/2022]
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Abstract
Moving past the discovery phase of proteomics, the term targeted proteomics combines multiple approaches investigating a certain set of proteins in more detail. One such targeted proteomics approach is the combination of liquid chromatography and selected or multiple reaction monitoring mass spectrometry (SRM, MRM). SRM-MS requires prior knowledge of the fragmentation pattern of peptides, as the presence of the analyte in a sample is determined by measuring the m/z values of predefined precursor and fragment ions. Using scheduled SRM-MS, many analytes can robustly be monitored allowing for high-throughput sample analysis of the same set of proteins over many conditions. In this chapter, fundaments of SRM-MS are explained as well as an optimized SRM pipeline from assay generation to data analyzed.
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Affiliation(s)
- H Alexander Ebhardt
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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Abstract
Standardization of hormone determinations is important because it simplifies interpretation of results and facilitates the use of common reference values for different assays. Progress in standardization has been achieved through the introduction of more homogeneous hormone standards for peptide and protein hormones. However, many automated methods for determinations of steroid hormones do not provide satisfactory result. Isotope dilution-mass spectrometry (ID-MS) has been used to establish reference methods for steroid hormone determinations and is now increasingly used for routine determinations of steroids and other low molecular weight compounds. Reference methods for protein hormones based on MS are being developed and these promise to improve standardization.
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Affiliation(s)
- Ulf-Håkan Stenman
- Department of Clinical Chemistry, Biomedicum, Helsinki University, PB 63, FIN-00014 Helsinki, Finland.
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50
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Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 2013; 5:2837-56. [DOI: 10.4155/bio.13.245] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Quantitative plasma proteomics, through the use of targeted MRM-MS and isotopically labeled standards, is emerging as a popular technique to address biological- and biomedical-centered queries. High precision and accuracy are essential in such measurements, particularly in protein biomarker research where translation to the clinic is sought. Standardized procedures and routine performance evaluation of all stages of the workflow (both pre-analytical and analytical) are therefore imperative to satisfy these requisites and enable high inter-laboratory reproducibility and transferability. In this review, we first discuss the pre-analytical and analytical variables that can affect the precision and accuracy of ‘absolute’ quantitative plasma proteomic measurements. Proposed strategies to limit such variability will then be highlighted and unmet needs for future exploration will be noted. Although there is no way to conduct a truly comprehensive review on this broad, rapidly changing topic, we have highlighted key aspects and included references to review articles on various sub-topics.
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