1
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Kuo CY, Zheng YF, Wang WC, Toh JT, Hsu YM, Chien HJ, Chang CJ, Lai CC. Direct Identification of Intact Proteins Using a Low-Resolution Mass Spectrometer with CID n/ETnoD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1507-1515. [PMID: 38905484 PMCID: PMC11228978 DOI: 10.1021/jasms.4c00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024]
Abstract
Over the past decades, proteomics has become increasingly important and a heavily discussed topic. The identification of intact proteins remains a major focus in this field. While most intact proteins are analyzed using high-resolution mass spectrometry, identifying them through low-resolution mass spectrometry continues to pose challenges. In our study, we investigated the capability of identifying various intact proteins using collision-induced dissociation (CID) and electron transfer without dissociation (ETnoD). Using myoglobin as our test protein, stable product ions were generated with CID, and the identities of the product ions were identified with ETnoD. ETnoD uses a short activation time (AcT, 5 ms) to create sequential charge-reduced precursor ion (CRI). The charges of the fragments and their sequences were determined with corresponding CRI. The product ions can be selected for subsequent CID (termed CIDn) combined with ETnoD for further sequence identification and validation. We refer to this method as CIDn/ETnoD. The use of a multistage CID activation (CIDn) and ETnoD protocol has been applied to several intact proteins to obtain multiple sequence identifications.
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Affiliation(s)
- Cheng-Yu Kuo
- Institute
of Molecular Biology, National Chung Hsing
University, Taichung 402, Taiwan
| | - Yi-Feng Zheng
- Institute
of Molecular Biology, National Chung Hsing
University, Taichung 402, Taiwan
| | - Wei-Chen Wang
- Institute
of Molecular Biology, National Chung Hsing
University, Taichung 402, Taiwan
| | - Jie-Teng Toh
- Institute
of Molecular Biology, National Chung Hsing
University, Taichung 402, Taiwan
| | - Yu-Ming Hsu
- Institute
of Molecular Biology, National Chung Hsing
University, Taichung 402, Taiwan
| | - Han-Ju Chien
- Department
of Biochemical Science and Technology, National
Chiayi University, Chiayi 600, Taiwan
| | - Chih-Jui Chang
- Department
of Molecular Biology and Human Genetics, Tzu Chi University, Hualien City 970, Taiwan
| | - Chien-Chen Lai
- Institute
of Molecular Biology, National Chung Hsing
University, Taichung 402, Taiwan
- Advanced
Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Graduate
Institute of Chinese Medical Science, China
Medical University, Taichung 406, Taiwan
- Doctoral
Program in Translational Medicine, National
Chung Hsing University, Taichung 402, Taiwan
- Rong
Hsing Translational Medicine Research Center, National Chung Hsing University, Taichung 402, Taiwan
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2
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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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3
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Gutierrez Reyes CD, Sanni A, Mogut D, Adeniyi M, Ahmadi P, Atashi M, Onigbinde S, Mechref Y. Targeted Analysis of Permethylated N-Glycans Using MRM/PRM Approaches. Methods Mol Biol 2024; 2762:251-266. [PMID: 38315370 DOI: 10.1007/978-1-0716-3666-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Targeted mass spectrometric analysis is widely employed across various omics fields as a validation strategy due to its high sensitivity and accuracy. The approach has been successfully employed for the structural analysis of proteins, glycans, lipids, and metabolites. Multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) have been the methods of choice for targeted structural studies of biomolecules. These target analyses simplify the analytical workflow, reduce background interference, and increase selectivity/specificity, allowing for a reliable quantification of permethylated N-glycans in complex biological matrices.
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Affiliation(s)
| | - Akeem Sanni
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Damir Mogut
- Department of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Moyinoluwa Adeniyi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
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4
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Gutierrez Reyes CD, Sanni A, Adeniyi M, Mogut D, Najera Gonzalez HR, Ahmadi P, Atashi M, Onigbinde S, Mechref Y. Targeted Glycoproteomics Analysis Using MRM/PRM Approaches. Methods Mol Biol 2024; 2762:231-250. [PMID: 38315369 DOI: 10.1007/978-1-0716-3666-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
MS-target analyses are frequently utilized to analyze and validate structural changes of biomolecules across diverse fields of study such as proteomics, glycoproteomics, glycomics, lipidomics, and metabolomics. Targeted studies are commonly conducted using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) techniques. A reliable glycoproteomics analysis in intricate biological matrices is possible with these techniques, which streamline the analytical workflow, lower background interference, and enhance selectivity and specificity.
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Affiliation(s)
| | - Akeem Sanni
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Moyinoluwa Adeniyi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Damir Mogut
- Department of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Hector R Najera Gonzalez
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
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5
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Xu H, Xu J, Liu X, Song W, Lyu X, Guo X, Hu W, Yang H, Wang L, Pan H, Chen J, Xing X, Zhu H, Sun W, Gong F. Serum metabolomics profiling of improved metabolic syndrome is characterized by decreased pro-inflammatory biomarkers: A longitudinal study in Chinese male adults. Nutr Res 2023; 115:13-25. [PMID: 37216838 DOI: 10.1016/j.nutres.2023.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Metabolic syndrome (MetS) is a serious global health concern. The objective of this study is to dynamically investigate the changes of metabolic profiles and metabolites in Chinese male MetS subjects after an 18 months diet and exercise intervention. Fifty male MetS patients defined according to International Diabetes Federation 2005 guidelines were subjected to diet and exercise counseling for 18 months. Serum samples were taken at baseline, 12 months, and 18 months, respectively, for clinical evaluation and metabolomics analyses. Diet and exercise intervention for 18 months achieved significant improvements in the metabolic profiles of all participants. Nineteen subjects (38.0%) exhibited MetS remission at the end of the study. A total of 812 relative features were characterized and 61 were successfully identified. Furthermore, 17 differential metabolites were of significance at both time points (baseline-12 months, baseline-18 months) and presented nonlinear trends through time. Eight metabolites (47.1%) were predominantly converged to inflammation and oxidative stress. Pro-inflammatory biomarkers were remarkably decreased after 18 months of intervention, and prostaglandin E2, neuroprotectin D1, and taxiphyllin in combination were firstly found to demonstrate a fair discriminative power (area under curve = 0.911) to predict the improvement of MetS undergone diet and exercise intervention. The significant shift of metabolomic profiling after 18 months of lifestyle counseling provide a novel insight and reveal that earlier inflammation control may be of potential benefit in MetS management.
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Affiliation(s)
- Hanyuan Xu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Department of Clinical Nutrition, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jiyu Xu
- Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Song
- Medical Science Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Xiaorui Lyu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaonan Guo
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Wenjing Hu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hongbo Yang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Linjie Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hui Pan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jichun Chen
- Nutrition Department, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, China
| | - Xiaoping Xing
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Huijuan Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| | - Wei Sun
- Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| | - Fengying Gong
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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6
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Mohammed Y, Goodlett D, Borchers CH. Absolute Quantitative Targeted Proteomics Assays for Plasma Proteins. Methods Mol Biol 2023; 2628:439-473. [PMID: 36781801 DOI: 10.1007/978-1-0716-2978-9_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Preclinical and clinical trials require rapid, precise, and multiplexed analytical methods to characterize the complex samples and to allow high-throughput biomarker monitoring with low consumption of sample material. Targeted proteomics has been used to address these challenges when quantifying protein abundances in complex biological matrices. In many of these studies, blood plasma is collected either as the main research or diagnostic sample or in combination with other specimens. Mass spectrometry (MS)-based targeted proteomics using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) with stable isotope-labeled internal standard (SIS) peptides allows robust characterization of blood plasma protein via absolute quantification. Compared to other commonly used technologies like enzyme-linked immunosorbent assay (ELISA), targeted proteomics is faster, more sensitive, and more cost-effective. Here we describe a protocol for the quantification of proteins in blood plasma using targeted MRM proteomics with heavy-labeled internal standards. The 270-protein panel allows rapid and robust absolute quantitative proteomic characterization of blood plasma in a 1 h gradient. The method we describe here works for non-depleted plasma, which makes it simple and easy to implement. Moreover, the protocol works with the two most commonly used blood plasma collection methods used in practice, namely, either K2EDTA or sodium citrate as anticoagulants.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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7
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Cho BG, Gutierrez Reyes CD, Goli M, Gautam S, Banazadeh A, Mechref Y. Targeted N-Glycan Analysis with Parallel Reaction Monitoring Using a Quadrupole-Orbitrap Hybrid Mass Spectrometer. Anal Chem 2022; 94:15215-15222. [DOI: 10.1021/acs.analchem.2c01975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | | | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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8
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van Duijl TT, Ruhaak LR, Smit NPM, Pieterse MM, Romijn FPHTM, Dolezal N, Drijfhout JW, de Fijter JW, Cobbaert CM. Development and Provisional Validation of a Multiplex LC-MRM-MS Test for Timely Kidney Injury Detection in Urine. J Proteome Res 2021; 20:5304-5314. [PMID: 34735145 PMCID: PMC8650098 DOI: 10.1021/acs.jproteome.1c00532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Kidney injury is
a complication frequently encountered in hospitalized
patients. Early detection of kidney injury prior to loss of renal
function is an unmet clinical need that should be targeted by a protein-based
biomarker panel. In this study, we aim to quantitate urinary kidney
injury biomarkers at the picomolar to nanomolar level by liquid chromatography
coupled to tandem mass spectrometry in multiple reaction monitoring
mode (LC-MRM-MS). Proteins were immunocaptured from urinary samples,
denatured, reduced, alkylated, and digested into peptides before LC-MRM-MS
analysis. Stable-isotope-labeled peptides functioned as internal standards,
and biomarker concentrations were attained by an external calibration
strategy. The method was evaluated for selectivity, carryover, matrix
effects, linearity, and imprecision. The LC-MRM-MS method enabled
the quantitation of KIM-1, NGAL, TIMP2, IGFBP7, CXCL9, nephrin, and
SLC22A2 and the detection of TGF-β1, cubilin, and uromodulin.
Two to three peptides were included per protein, and three transitions
were monitored per peptide for analytical selectivity. The analytical
carryover was <1%, and minimal urine matrix effects were observed
by combining immunocapture and targeted LC-MRM-MS analysis. The average
total CV of all quantifier peptides was 26%. The linear measurement
range was determined per measurand and found to be 0.05–30
nmol/L. The targeted MS-based method enables the multiplex quantitation
of low-abundance urinary kidney injury biomarkers for future clinical
evaluation.
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Affiliation(s)
- Tirsa T van Duijl
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Mervin M Pieterse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Natasja Dolezal
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Johan W de Fijter
- Department of Nephrology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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9
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Identification of cortactin molecular forms in human urine and their possible diagnostic value. UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.04.103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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10
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Nguyen N, Souza T, Verheijen MCT, Gmuender H, Selevsek N, Schlapbach R, Kleinjans J, Jennen D. Translational Proteomics Analysis of Anthracycline-Induced Cardiotoxicity From Cardiac Microtissues to Human Heart Biopsies. Front Genet 2021; 12:695625. [PMID: 34211507 PMCID: PMC8239409 DOI: 10.3389/fgene.2021.695625] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/24/2021] [Indexed: 01/17/2023] Open
Abstract
Anthracyclines, including doxorubicin, idarubicin, and epirubicin, are common antitumor drugs as well as well-known cardiotoxic agents. This study analyzed the proteomics alteration in cardiac tissues caused by these 3 anthracyclines analogs. The in vitro human cardiac microtissues were exposed to drugs in 2 weeks; the proteomic data were measured at 7 time points. The heart biopsy data were collected from heart failure patients, in which some patients underwent anthracycline treatment. The anthracyclines-affected proteins were separately identified in the in vitro and in vivo dataset using the WGCNA method. These proteins engage in different cellular pathways including translation, metabolism, mitochondrial function, muscle contraction, and signaling pathways. From proteins detected in 2 datasets, a protein-protein network was established with 4 hub proteins, and 7 weighted proteins from both cardiac microtissue and human biopsies data. These 11 proteins, which involve in mitochondrial functions and the NF-κB signaling pathway, could provide insights into the anthracycline toxic mechanism. Some of them, such as HSPA5, BAG3, and SH3BGRL, are cardiac therapy targets or cardiotoxicity biomarkers. Other proteins, such as ATP5F1B and EEF1D, showed similar responses in both the in vitro and in vivo data. This suggests that the in vitro outcomes could link to clinical phenomena in proteomic analysis.
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Affiliation(s)
- Nhan Nguyen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Terezinha Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Marcha C T Verheijen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | | | | | - Ralph Schlapbach
- Functional Genomics Center, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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11
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Network integration and modelling of dynamic drug responses at multi-omics levels. Commun Biol 2020; 3:573. [PMID: 33060801 PMCID: PMC7567116 DOI: 10.1038/s42003-020-01302-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 09/14/2020] [Indexed: 12/25/2022] Open
Abstract
Uncovering cellular responses from heterogeneous genomic data is crucial for molecular medicine in particular for drug safety. This can be realized by integrating the molecular activities in networks of interacting proteins. As proof-of-concept we challenge network modeling with time-resolved proteome, transcriptome and methylome measurements in iPSC-derived human 3D cardiac microtissues to elucidate adverse mechanisms of anthracycline cardiotoxicity measured with four different drugs (doxorubicin, epirubicin, idarubicin and daunorubicin). Dynamic molecular analysis at in vivo drug exposure levels reveal a network of 175 disease-associated proteins and identify common modules of anthracycline cardiotoxicity in vitro, related to mitochondrial and sarcomere function as well as remodeling of extracellular matrix. These in vitro-identified modules are transferable and are evaluated with biopsies of cardiomyopathy patients. This to our knowledge most comprehensive study on anthracycline cardiotoxicity demonstrates a reproducible workflow for molecular medicine and serves as a template for detecting adverse drug responses from complex omics data. Using a network propagation approach with integrated multi-omic data, Selevsek et al. develop a reproducible workflow for identifying drug toxicity effects in cellular systems. This is demonstrated with the analysis of anthracycline cardiotoxicity in cardiac microtissues under the effect of multiple drugs.
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12
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Ayciriex S, Carrière R, Bardet C, Blanc JCYL, Salvador A, Fortin T, Lemoine J. Streamlined Development of Targeted Mass Spectrometry‐Based Method Combining Scout‐MRM and a Web‐Based Tool Indexed with Scout Peptides. Proteomics 2020; 20:e1900254. [DOI: 10.1002/pmic.201900254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 12/10/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Sophie Ayciriex
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
| | - Romain Carrière
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
| | - Chloé Bardet
- Anaquant 5 rue de la Doua F‐69100 Villeurbanne France
| | | | - Arnaud Salvador
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
| | - Tanguy Fortin
- Anaquant 5 rue de la Doua F‐69100 Villeurbanne France
| | - Jérôme Lemoine
- Univ Lyon, CNRSUniversité Claude Bernard Lyon 1ENS de LyonInstitut des Sciences AnalytiquesUMR 5280 5 rue de la Doua F‐69100 Villeurbanne France
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13
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A new paradigm in public health assessment: Water fingerprinting for protein markers of public health using mass spectrometry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115621] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Cilento EM, Jin L, Stewart T, Shi M, Sheng L, Zhang J. Mass spectrometry: A platform for biomarker discovery and validation for Alzheimer's and Parkinson's diseases. J Neurochem 2019; 151:397-416. [PMID: 30474862 DOI: 10.1111/jnc.14635] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022]
Abstract
Accurate, reliable, and objective biomarkers for Alzheimer's disease (AD), Parkinson's disease (PD), and related age-associated neurodegenerative disorders are urgently needed to assist in both diagnosis, particularly at early stages, and monitoring of disease progression. Technological advancements in protein detection platforms over the last few decades have resulted in a plethora of reported molecular biomarker candidates for both AD and PD; however, very few of these candidates are developed beyond the discovery phase of the biomarker development pipeline, a reflection of the current bottleneck within the field. In this review, the expanded use of selected reaction monitoring (SRM) targeted mass spectrometry will be discussed in detail as a platform for systematic verification of large panels of protein biomarker candidates prior to costly validation testing. We also advocate for the coupling of discovery-based proteomics with modern targeted MS-based approaches (e.g., SRM) within a single study in future workflows to expedite biomarker development and validation for AD and PD. It is our hope that improving the efficiency within the biomarker development process by use of an SRM pipeline may ultimately hasten the development of biomarkers that both decrease misdiagnosis of AD and PD and ultimately lead to detection at early stages of disease and objective assessment of disease progression. This article is part of the special issue "Proteomics".
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Affiliation(s)
- Eugene M Cilento
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lorrain Jin
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Tessandra Stewart
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Min Shi
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lifu Sheng
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Jing Zhang
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA.,Department of Pathology, School of Basic Medicine, Peking University Health Science Center, Peking University Third Hospital and Peking Key Laboratory for Early Diagnosis of Neurodegenerative Disorders, Beijing, China
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15
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Mohammed Y, Pan J, Zhang S, Han J, Borchers CH. ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments. Proteomics Clin Appl 2018; 12:1600180. [PMID: 28895300 PMCID: PMC6084352 DOI: 10.1002/prca.201600180] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/09/2017] [Indexed: 11/08/2022]
Abstract
PURPOSE Targeted proteomics using MRM with stable-isotope-labeled internal-standard (SIS) peptides is the current method of choice for protein quantitation in complex biological matrices. Better quantitation can be achieved with the internal standard-addition method, where successive increments of synthesized natural form (NAT) of the endogenous analyte are added to each sample, a response curve is generated, and the endogenous concentration is determined at the x-intercept. Internal NAT-addition, however, requires multiple analyses of each sample, resulting in increased sample consumption and analysis time. EXPERIMENTAL DESIGN To compare the following three methods, an MRM assay for 34 high-to-moderate abundance human plasma proteins is used: classical internal SIS-addition, internal NAT-addition, and external NAT-addition-generated in buffer using NAT and SIS peptides. Using endogenous-free chicken plasma, the accuracy is also evaluated. RESULTS The internal NAT-addition outperforms the other two in precision and accuracy. However, the curves derived by internal vs. external NAT-addition differ by only ≈3.8% in slope, providing comparable accuracies and precision with good CV values. CONCLUSIONS AND CLINICAL RELEVANCE While the internal NAT-addition method may be "ideal", this new external NAT-addition can be used to determine the concentration of high-to-moderate abundance endogenous plasma proteins, providing a robust and cost-effective alternative for clinical analyses or other high-throughput applications.
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Affiliation(s)
- Yassene Mohammed
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenthe Netherlands
| | - Jingxi Pan
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Suping Zhang
- MRM Proteomics Inc.VictoriaBritish ColumbiaCanada
| | - Jun Han
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Christoph H. Borchers
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- University of VictoriaDepartment of Biochemistry and MicrobiologyVictoriaBCCanada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQuebecCanada
- Proteomics CentreSegal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQuebecCanada
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16
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Bijen HM, Hassan C, Kester MGD, Janssen GMC, Hombrink P, de Ru AH, Drijfhout JW, Meiring HD, de Jong AP, Falkenburg JHF, Jimenez CR, Heemskerk MHM, van Veelen PA. Specific T Cell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface. Proteomics 2018; 18:e1700250. [PMID: 29251415 DOI: 10.1002/pmic.201700250] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/22/2017] [Indexed: 12/20/2022]
Abstract
Allogeneic stem cell transplantation has emerged as immunotherapy in the treatment of a variety of hematological malignancies. Its efficacy depends on induction of graft versus leukemia by donor lymphocytes. Both graft versus leukemia and graft versus host disease are induced by T cells reactive against polymorphic peptides, called minor histocompatibility antigens (MiHA), which differ between patient and donor and are presented in the context of self-HLA (where HLA is human leukocyte antigen). The allelic counterpart (AC) of the MiHA is generally considered to be absent at the cell surface, based on the absence of immune responses directed against the AC. To study this in detail, we evaluate the recognition, HLA-binding affinity, and cell surface expression of three selected MiHA. By quantitative MS, we demonstrate the similarly abundant expression of both MiHA and AC at the cell surface. We conclude that the absent recognition of the AC cannot generally be explained by insufficient processing and presentation at the cell surface of the AC.
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Affiliation(s)
- Helena M Bijen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chopie Hassan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pleun Hombrink
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hugo D Meiring
- Laboratory for Vaccine Research, Unit Research and Development, Netherlands Vaccine Institute, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ad P de Jong
- Laboratory for Vaccine Research, Unit Research and Development, Netherlands Vaccine Institute, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Connie R Jimenez
- OncoProteomics Laboratory, Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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17
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Chen YT, Chen HW, Wu CF, Chu LJ, Chiang WF, Wu CC, Yu JS, Tsai CH, Liang KH, Chang YS, Wu M, Ou Yang WT. Development of a Multiplexed Liquid Chromatography Multiple-Reaction-Monitoring Mass Spectrometry (LC-MRM/MS) Method for Evaluation of Salivary Proteins as Oral Cancer Biomarkers. Mol Cell Proteomics 2017; 16:799-811. [PMID: 28235782 PMCID: PMC5417822 DOI: 10.1074/mcp.m116.064758] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 02/22/2017] [Indexed: 11/06/2022] Open
Abstract
Multiple (selected) reaction monitoring (MRM/SRM) of peptides is a growing technology for target protein quantification because it is more robust, precise, accurate, high-throughput, and multiplex-capable than antibody-based techniques. The technique has been applied clinically to the large-scale quantification of multiple target proteins in different types of fluids. However, previous MRM-based studies have placed less focus on sample-preparation workflow and analytical performance in the precise quantification of proteins in saliva, a noninvasively sampled body fluid. In this study, we evaluated the analytical performance of a simple and robust multiple reaction monitoring (MRM)-based targeted proteomics approach incorporating liquid chromatography with mass spectrometry detection (LC-MRM/MS). This platform was used to quantitatively assess the biomarker potential of a group of 56 salivary proteins that have previously been associated with human cancers. To further enhance the development of this technology for assay of salivary samples, we optimized the workflow for salivary protein digestion and evaluated quantification performance, robustness and technical limitations in analyzing clinical samples. Using a clinically well-characterized cohort of two independent clinical sample sets (total n = 119), we quantitatively characterized these protein biomarker candidates in saliva specimens from controls and oral squamous cell carcinoma (OSCC) patients. The results clearly showed a significant elevation of most targeted proteins in saliva samples from OSCC patients compared with controls. Overall, this platform was capable of assaying the most highly multiplexed panel of salivary protein biomarkers, highlighting the clinical utility of MRM in oral cancer biomarker research.
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Affiliation(s)
- Yi-Ting Chen
- From the ‡Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan;
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- ‖Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Hsiao-Wei Chen
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Feng Wu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lichieh Julie Chu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- **Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wei-Fang Chiang
- ‡‡Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan
- §§School of Dentistry, National Yang Ming University, Taipei, Taiwan
| | - Chih-Ching Wu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶¶Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- ‖‖Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Jau-Song Yu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- **Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Cheng-Han Tsai
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kung-Hao Liang
- **Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yu-Sun Chang
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- ¶Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- ‖‖Department of Otolaryngology - Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Maureen Wu
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Ting Ou Yang
- §Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
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18
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A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition. Anal Chim Acta 2017; 964:7-23. [DOI: 10.1016/j.aca.2017.01.059] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 01/18/2023]
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19
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Matondo M, Marcellin M, Chaoui K, Bousquet-Dubouch MP, Gonzalez-de-Peredo A, Monsarrat B, Burlet-Schiltz O. Determination of differentially regulated proteins upon proteasome inhibition in AML cell lines by the combination of large-scale and targeted quantitative proteomics. Proteomics 2017; 17:1600089. [PMID: 27709814 PMCID: PMC5396343 DOI: 10.1002/pmic.201600089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 09/05/2016] [Accepted: 10/14/2016] [Indexed: 01/08/2023]
Abstract
The ubiquitin-proteasome pathway (UPP) plays a critical role in the degradation of proteins implicated in cell cycle control, signal transduction, DNA damage response, apoptosis and immune response. Proteasome inhibitors can inhibit the growth of a broad spectrum of human cancer cells by altering the balance of intracellular proteins. However, the targets of these compounds in acute myeloid leukemia (AML) cells have not been fully characterized. Herein, we combined large-scale quantitative analysis by SILAC-MS and targeted quantitative proteomic analysis in order to identify proteins regulated upon proteasome inhibition in two AML cell lines displaying different stages of maturation: immature KG1a cells and mature U937 cells. In-depth data analysis enabled accurate quantification of more than 7000 proteins in these two cell lines. Several candidates were validated by selected reaction monitoring (SRM) measurements in a large number of samples. Despite the broad range of proteins known to be affected by proteasome inhibition, such as heat shock (HSP) and cell cycle proteins, our analysis identified new differentially regulated proteins, including IL-32, MORF family mortality factors and apoptosis inducing factor SIVA, a target of p53. It could explain why proteasome inhibitors induce stronger apoptotic responses in immature AML cells.
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Affiliation(s)
- Mariette Matondo
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Marlène Marcellin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Karima Chaoui
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | | | - Anne Gonzalez-de-Peredo
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Bernard Monsarrat
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
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20
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Uzozie AC, Selevsek N, Wahlander A, Nanni P, Grossmann J, Weber A, Buffoli F, Marra G. Targeted Proteomics for Multiplexed Verification of Markers of Colorectal Tumorigenesis. Mol Cell Proteomics 2017; 16:407-427. [PMID: 28062797 DOI: 10.1074/mcp.m116.062273] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
Targeted proteomic methods can accelerate the verification of multiple tumor marker candidates in large series of patient samples. We utilized the targeted approach known as selected/multiple reaction monitoring (S/MRM) to verify potential protein markers of colorectal adenoma identified by our group in previous transcriptomic and quantitative shotgun proteomic studies of a large cohort of precancerous colorectal lesions. We developed SRM assays to reproducibly detect and quantify 25 (62.5%) of the 40 selected proteins in an independent series of precancerous and cancerous tissue samples (19 adenoma/normal mucosa pairs; 17 adenocarcinoma/normal mucosa pairs). Twenty-three proteins were significantly up-regulated (n = 17) or downregulated (n = 6) in adenomas and/or adenocarcinomas, as compared with normal mucosa (linear fold changes ≥ ±1.3, adjusted p value <0.05). Most changes were observed in both tumor types (up-regulation of ANP32A, ANXA3, SORD, LDHA, LCN2, NCL, S100A11, SERPINB5, CDV3, OLFM4, and REG4; downregulation of ARF6 and PGM5), and a five-protein biomarker signature distinguished neoplastic tissue from normal mucosa with a maximum area under the receiver operating curve greater than 0.83. Other changes were specific for adenomas (PPA1 and PPA2 up-regulation; KCTD12 downregulation) or adenocarcinoma (ANP32B, G6PD, RCN1, and SET up-regulation; downregulated AKR1B1, APEX1, and PPA1). Some changes significantly correlated with a few patient- or tumor-related phenotypes. Twenty-two (96%) of the 23 proteins have a potential to be released from the tumors into the bloodstream, and their detectability in plasma has been previously reported. The proteins identified in this study expand the pool of biomarker candidates that can be used to develop a standardized precolonoscopy blood test for the early detection of colorectal tumors.
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Affiliation(s)
| | - Nathalie Selevsek
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Asa Wahlander
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Paolo Nanni
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Achim Weber
- ¶Institute of Surgical Pathology, University of Zurich, Switzerland
| | - Federico Buffoli
- ‖ Gastroenterology and Endoscopy Unit, Hospital of Cremona, Italy
| | - Giancarlo Marra
- From the ‡Institute of Molecular Cancer Research, University of Zurich, Switzerland;
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21
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Gao Y, Wang H, Nicora CD, Shi T, Smith RD, Sigdel TK, Sarwal MM, Camp DG, Qian WJ. LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers. Methods Mol Biol 2017; 1788:145-156. [PMID: 29116567 DOI: 10.1007/7651_2017_93] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Liquid chromatography (LC)-selected reaction monitoring (SRM) is a powerful protein quantification technique in terms of sensitivity, reproducibility, and multiplexing capability. LC-SRM can accurately measure the concentrations of surrogate proteotypic peptides for targeted proteins in complex biological samples by using their stable heavy isotope-labeled counterparts as internal standards. Herein, we describe a step-by-step protocol of the application of LC-SRM to quantify candidate protein biomarkers in human urine.
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Affiliation(s)
- Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hui Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tara K Sigdel
- The Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Minnie M Sarwal
- The Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David G Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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22
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Mohammed Y, Bhowmick P, Smith DS, Domanski D, Jackson AM, Michaud SA, Malchow S, Percy AJ, Chambers AG, Palmer A, Zhang S, Sickmann A, Borchers CH. PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues. Proteomics 2016; 17. [PMID: 27683069 DOI: 10.1002/pmic.201600210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/31/2016] [Accepted: 09/27/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Yassene Mohammed
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pallab Bhowmick
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Derek S Smith
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Dominik Domanski
- Molecular Pathology, JGH Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
| | - Angela M Jackson
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Sarah A Michaud
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
| | - Andrew J Percy
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Andrew G Chambers
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Andrea Palmer
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Suping Zhang
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
- Molecular Pathology, JGH Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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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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Zhang H, Li J. From Cytosol to the Apoplast: The Hygromycin Phosphotransferase (HYG(R)) Model in Arabidopsis. Methods Mol Biol 2016; 1459:81-90. [PMID: 27665552 DOI: 10.1007/978-1-4939-3804-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
The process by which proteins are secreted via endoplasmic reticulum (ER)/Golgi-independent mechanism is conveniently called unconventional protein secretion. Recent studies have revealed that unconventional protein secretion operates in plants, but little is known about its underlying mechanism and function. This chapter provides methods we have used to analyze unconventional character of hygromycin phosphotransferase (HYG(R)) secretion in plant cells. Following isolation of protoplasts from HYG (R) -GFP-transgenic plants and incubation with brefeldin A (BFA), an inhibitor of conventional secretory pathway, we easily obtain protein extracts from protoplasts and culture medium separately. These proteins are separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by Western blot analysis with anti-GFP antibodies.
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Affiliation(s)
- Haiyan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Jinjin Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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25
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Calderón-Celis F, Diez-Fernández S, Costa-Fernández JM, Encinar JR, Calvete JJ, Sanz-Medel A. Elemental Mass Spectrometry for Absolute Intact Protein Quantification without Protein-Specific Standards: Application to Snake Venomics. Anal Chem 2016; 88:9699-9706. [PMID: 27593495 DOI: 10.1021/acs.analchem.6b02585] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Absolute protein quantification methods based on molecular mass spectrometry usually require stable isotope-labeled analogous standards for each target protein or peptide under study, which in turn must be certified using natural standards. In this work, we report a direct and accurate methodology based on capLC-ICP-QQQ and online isotope dilution analysis for the absolute and sensitive quantification of intact proteins. The combination of the postcolumn addition of 34S and a generic S-containing internal standard spiked to the sample provides full compound independent detector response and thus protein quantification without the need for specific standards. Quantitative recoveries, using a chromatographic core-shell C4 column for the various protein species assayed were obtained (96-100%). Thus, the proposed strategy enables the accurate quantification of proteins even if no specific standards are available for them. In addition, to the best of our knowledge, we obtained the lowest detection limits reported in the quantitative analysis of intact proteins by direct measurement of sulfur with ICPMS (358 fmol) and protein (ranging from 7 to 15 fmol depending on the assayed protein). The quantitative results for individual and simple mixtures of model proteins were statistically indistinguishable from the manufacturer's values. Finally, the suitability of the strategy for real sample analysis (including quantitative protein recovery from the column) was illustrated for the individual absolute quantification of the proteins and whole protein content in a venom sample. Parallel capLC-ESI-QTOF analysis was employed to identify the proteins, a prerequisite to translate the mass of quantified S for each chromatographic peak into individual protein mass.
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Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Silvia Diez-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas (CSIC), Jaume Roig 11, 46010 Valencia, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo , Julián Clavería 8, 33006 Oviedo, Spain
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26
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Konvalinka A, Batruch I, Tokar T, Dimitromanolakis A, Reid S, Song X, Pei Y, Drabovich AP, Diamandis EP, Jurisica I, Scholey JW. Quantification of angiotensin II-regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring. Clin Proteomics 2016; 13:16. [PMID: 27499720 PMCID: PMC4974759 DOI: 10.1186/s12014-016-9117-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 06/23/2016] [Indexed: 12/24/2022] Open
Abstract
Background Angiotensin-II (Ang II) mediates progression of autosomal-dominant polycystic kidney disease (ADPKD) and other chronic kidney diseases (CKD). However, markers of kidney Ang II activity are lacking. We previously defined 83 Ang II-regulated proteins in vitro, which reflected kidney Ang II activity in vivo. Methods In this study, we developed selected reaction monitoring (SRM) assays for quantification of Ang II-regulated proteins in urine of ADPKD and CKD patients. We demonstrated that 47 of 83 Ang II-regulated transcripts were differentially expressed in cystic compared to normal kidney tissue. We then developed SRM assays for 18 Ang II-regulated proteins overexpressed in cysts and/or secreted in urine. Methods that yielded CV ≤ 6 % for control proteins, and recovery ~100 % were selected. Heavy-labeled peptides corresponding to 13 identified Ang II-regulated peptides were spiked into urine samples of 17 ADPKD patients, 9 patients with CKD predicted to have high kidney Ang II activity and 11 healthy subjects. Samples were then digested and analyzed on triple-quadrupole mass spectrometer in duplicates. Resluts Calibration curves demonstrated linearity (R2 > 0.99) and within-run CVs < 9 % in the concentration range of 7/13 peptides. Peptide concentrations were normalized by urine creatinine. Deamidated peptide forms were monitored, and accounted for <15 % of the final concentrations. Urine excretion rates of proteins BST1, LAMB2, LYPA1, RHOB and TSP1 were significantly different (p < 0.05, one-way ANOVA) between patients with CKD, those with ADPKD and healthy controls. Urine protein excretion rates were highest in CKD patients and lowest in ADPKD patients. Univariate analysis demonstrated significant association between urine protein excretion rates of most proteins and disease group (p < 0.05, ANOVA) as well as sex (p < 0.05, unpaired t test). Multivariate analysis across protein concentration, age and sex demonstrated good separation between ADPKD and CKD patients. Conclusions We have optimized methods for quantification of Ang II-regulated proteins, and we demonstrated that they reflected differences in underlying kidney disease in this pilot study. High urine excretion of Ang II-regulated proteins in CKD patients likely reflects high kidney Ang II activity. Low excretion in ADPKD appears related to lack of communication between cysts and tubules. Future studies will determine whether urine excretion rate of Ang II-regulated proteins correlates with kidney Ang II activity in larger cohorts of chronic kidney disease patients. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9117-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Konvalinka
- Division of Nephrology, Department of Medicine, Toronto General Hospital, University Health Network, University of Toronto, 11-PMB-189, 585 University Avenue, Toronto, ON M5G 2N2 Canada ; Toronto General Research Institute, University Health Network, Toronto, Canada
| | - Ihor Batruch
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Tomas Tokar
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Apostolos Dimitromanolakis
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Shelby Reid
- Toronto General Research Institute, University Health Network, Toronto, Canada
| | - Xuewen Song
- Division of Genomic Medicine, University Health Network, University of Toronto, Toronto, Canada
| | - York Pei
- Division of Nephrology, Department of Medicine, Toronto General Hospital, University Health Network, University of Toronto, 11-PMB-189, 585 University Avenue, Toronto, ON M5G 2N2 Canada ; Toronto General Research Institute, University Health Network, Toronto, Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada ; Department of Clinical Biochemistry, University Health Network, University of Toronto, Toronto, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada ; Departments of Medical Biophysics and Computer Science, University Health Network, University of Toronto, Toronto, Canada
| | - James W Scholey
- Division of Nephrology, Department of Medicine, Toronto General Hospital, University Health Network, University of Toronto, 11-PMB-189, 585 University Avenue, Toronto, ON M5G 2N2 Canada ; Toronto General Research Institute, University Health Network, Toronto, Canada
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27
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Starodubtseva NL, Kononikhin AS, Bugrova AE, Chagovets V, Indeykina M, Krokhina KN, Nikitina IV, Kostyukevich YI, Popov IA, Larina IM, Timofeeva LA, Frankevich VE, Ionov OV, Degtyarev DN, Nikolaev EN, Sukhikh GT. Investigation of urine proteome of preterm newborns with respiratory pathologies. J Proteomics 2016; 149:31-37. [PMID: 27321582 DOI: 10.1016/j.jprot.2016.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/23/2016] [Accepted: 06/10/2016] [Indexed: 12/27/2022]
Abstract
A serious problem during intensive care and nursing of premature infants is the invasiveness of many examination methods. Urine is an excellent source of potential biomarkers due to the safety of the collection procedure. The purpose of this study was to determine the features specific for the urine proteome of preterm newborns and their changes under respiratory pathologies of infectious and non-infectious origin. The urine proteome of 37 preterm neonates with respiratory diseases and 10 full-term newborns as a control group were investigated using the LC-MS/MS method. The total number of identified proteins and unique peptides was 813 and 3672 respectively. In order to further specify the defined infant-specific dataset these proteins were compared with urine proteome of healthy adults (11 men and 11 pregnant women) resulting in 94 proteins found only in infants. Pairwise analysis performed for label-free proteomic data revealed 36 proteins which reliably distinguished newborns with respiratory disorders of infectious genesis from those with non-infectious pathologies, including: proteins involved in cell adhesion (CDH-2,-5,-11, NCAM1, TRY1, DSG2), metabolism (LAMP1, AGRN, TPP1, GPX3, APOD, CUBN, IDH1), regulation of enzymatic activity (SERPINA4, VASN, GAPDH), inflammatory and stress response (CD55, CD 93, NGAL, HP, TNFR, LCN2, AGT, S100P, SERPINA1/C1/B1/F1).
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Affiliation(s)
- Natalia L Starodubtseva
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia
| | - Alexey S Kononikhin
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia
| | - Anna E Bugrova
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Vitaliy Chagovets
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Maria Indeykina
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
| | - Ksenia N Krokhina
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Irina V Nikitina
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Yury I Kostyukevich
- Moscow Institute of Physics and Technology, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
| | - Igor A Popov
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia
| | - Irina M Larina
- Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia
| | - Leila A Timofeeva
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vladimir E Frankevich
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Oleg V Ionov
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Dmitry N Degtyarev
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Eugene N Nikolaev
- Moscow Institute of Physics and Technology, Moscow, Russia; Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskij pr. 38 k.2, 119334 Moscow, Russia.
| | - Gennady T Sukhikh
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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28
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Development and characterization of a pseudo multiple reaction monitoring method for the quantification of human uromodulin in urine. Bioanalysis 2016; 8:1279-96. [DOI: 10.4155/bio-2016-0055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: Uromodulin is the most abundant protein in healthy human urine. Recently it has been suggested as a specific biomarker of renal tubular damage. We have developed a novel pseudo multiple reaction monitoring (pseudo MRM) for the protein's quantification in human urine. Results: Selection of two peptides allowed quantification of uromodulin in human urine. The pseudo MRM quantified uromodulin in healthy individuals between 21 and 1344 nM and in autosomal dominant tubulointerstitial kidney disease-UMOD patients between 2 and 25 nM. Conclusion: The pseudo MRM allows greater confidence in assay specificity than traditional MRM methods and quantified uromodulin at concentrations higher than achievable by ELISA. Differences in urinary uromodulin concentration related to the rs4293393 promoter variant in the UMOD gene was confirmed. This method will be used to further investigate uromodulin as a biomarker of renal injury.
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29
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Wang EH, Combe PC, Schug KA. Multiple Reaction Monitoring for Direct Quantitation of Intact Proteins Using a Triple Quadrupole Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:886-896. [PMID: 26956437 DOI: 10.1007/s13361-016-1368-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
Methods that can efficiently and effectively quantify proteins are needed to support increasing demand in many bioanalytical fields. Triple quadrupole mass spectrometry (QQQ-MS) is sensitive and specific, and it is routinely used to quantify small molecules. However, low resolution fragmentation-dependent MS detection can pose inherent difficulties for intact proteins. In this research, we investigated variables that affect protein and fragment ion signals to enable protein quantitation using QQQ-MS. Collision induced dissociation gas pressure and collision energy were found to be the most crucial variables for optimization. Multiple reaction monitoring (MRM) transitions for seven standard proteins, including lysozyme, ubiquitin, cytochrome c from both equine and bovine, lactalbumin, myoglobin, and prostate-specific antigen (PSA) were determined. Assuming the eventual goal of applying such methodology is to analyze protein in biological fluids, a liquid chromatography method was developed. Calibration curves of six standard proteins (excluding PSA) were obtained to show the feasibility of intact protein quantification using QQQ-MS. Linearity (2-3 orders), limits of detection (0.5-50 μg/mL), accuracy (<5% error), and precision (1%-12% CV) were determined for each model protein. Sensitivities for different proteins varied considerably. Biological fluids, including human urine, equine plasma, and bovine plasma were used to demonstrate the specificity of the approach. The purpose of this model study was to identify, study, and demonstrate the advantages and challenges for QQQ-MS-based intact protein quantitation, a largely underutilized approach to date.
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Affiliation(s)
- Evelyn H Wang
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Peter C Combe
- Shimadzu Scientific Instruments, Inc., Columbia, MD, 21046, USA
| | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA.
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30
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Zhou L, Wang K, Li Q, Nice EC, Zhang H, Huang C. Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives. Expert Rev Proteomics 2016; 13:367-81. [PMID: 26923776 DOI: 10.1586/14789450.2016.1159959] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.
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Affiliation(s)
- Li Zhou
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Kui Wang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Qifu Li
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Edouard C Nice
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
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31
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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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32
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Steffen P, Kwiatkowski M, Robertson WD, Zarrine-Afsar A, Deterra D, Richter V, Schlüter H. Protein species as diagnostic markers. J Proteomics 2016; 134:5-18. [DOI: 10.1016/j.jprot.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
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33
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Khristenko NA, Larina IM, Domon B. Longitudinal Urinary Protein Variability in Participants of the Space Flight Simulation Program. J Proteome Res 2015; 15:114-24. [DOI: 10.1021/acs.jproteome.5b00594] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nina A. Khristenko
- Luxembourg
Clinical Proteomics Center (LCP), Luxembourg Institute of Health, Strassen 1445, Luxembourg
- University of Luxembourg, Esch-sur-Alzette 4365, Luxembourg
| | | | - Bruno Domon
- Luxembourg
Clinical Proteomics Center (LCP), Luxembourg Institute of Health, Strassen 1445, Luxembourg
- University of Luxembourg, Esch-sur-Alzette 4365, Luxembourg
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34
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Mermelekas G, Vlahou A, Zoidakis J. SRM/MRM targeted proteomics as a tool for biomarker validation and absolute quantification in human urine. Expert Rev Mol Diagn 2015; 15:1441-54. [DOI: 10.1586/14737159.2015.1093937] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Pernikářová V, Bouchal P. Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps. Expert Rev Proteomics 2015; 12:651-67. [PMID: 26456120 DOI: 10.1586/14789450.2015.1094381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The concept of personalized medicine includes novel protein biomarkers that are expected to improve the early detection, diagnosis and therapy monitoring of malignant diseases. Tissues, biofluids, cell lines and xenograft models are the common sources of biomarker candidates that require verification of clinical value in independent patient cohorts. Targeted proteomics - based on selected reaction monitoring, or data extraction from data-independent acquisition based digital maps - now represents a promising mass spectrometry alternative to immunochemical methods. To date, it has been successfully used in a high number of studies answering clinical questions on solid malignancies: breast, colorectal, prostate, ovarian, endometrial, pancreatic, hepatocellular, lung, bladder and others. It plays an important role in functional proteomic experiments that include studying the role of post-translational modifications in cancer progression. This review summarizes verified biomarker candidates successfully quantified by targeted proteomics in this field and directs the readers who plan to design their own hypothesis-driven experiments to appropriate sources of methods and knowledge.
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Affiliation(s)
- Vendula Pernikářová
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic
| | - Pavel Bouchal
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic.,b Masaryk Memorial Cancer Institute , Regional Centre for Applied Molecular Oncology , Žlutý kopec 7, 65653 Brno , Czech Republic
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36
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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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37
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Percy AJ, Yang J, Hardie DB, Chambers AG, Tamura-Wells J, Borchers CH. Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies. Methods 2015; 81:24-33. [DOI: 10.1016/j.ymeth.2015.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/13/2015] [Accepted: 04/01/2015] [Indexed: 01/01/2023] Open
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38
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Identification and validation of potential new biomarkers for prostate cancer diagnosis and prognosis using 2D-DIGE and MS. BIOMED RESEARCH INTERNATIONAL 2015; 2015:454256. [PMID: 25667921 PMCID: PMC4312578 DOI: 10.1155/2015/454256] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/05/2014] [Accepted: 09/05/2014] [Indexed: 12/14/2022]
Abstract
This study was designed to identify and validate potential new biomarkers for prostate cancer and to distinguish patients with and without biochemical relapse. Prostate tissue samples analyzed by 2D-DIGE (two-dimensional difference in gel electrophoresis) and mass spectrometry (MS) revealed downregulation of secernin-1 (P < 0.044) in prostate cancer, while vinculin showed significant upregulation (P < 0.001). Secernin-1 overexpression in prostate tissue was validated using Western blot and immunohistochemistry while vinculin expression was validated using immunohistochemistry. These findings indicate that secernin-1 and vinculin are potential new tissue biomarkers for prostate cancer diagnosis and prognosis, respectively. For validation, protein levels in urine were also examined by Western blot analysis. Urinary vinculin levels in prostate cancer patients were significantly higher than in urine from nontumor patients (P = 0.006). Using multiple reaction monitoring-MS (MRM-MS) analysis, prostatic acid phosphatase (PAP) showed significant higher levels in the urine of prostate cancer patients compared to controls (P = 0.012), while galectin-3 showed significant lower levels in the urine of prostate cancer patients with biochemical relapse, compared to those without relapse (P = 0.017). Three proteins were successfully differentiated between patients with and without prostate cancer and patients with and without relapse by using MRM. Thus, this technique shows promise for implementation as a noninvasive clinical diagnostic technique.
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39
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Shi M, Movius J, Dator R, Aro P, Zhao Y, Pan C, Lin X, Bammler TK, Stewart T, Zabetian CP, Peskind ER, Hu SC, Quinn JF, Galasko DR, Zhang J. Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation. Mol Cell Proteomics 2015; 14:544-55. [PMID: 25556233 DOI: 10.1074/mcp.m114.040576] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Finding robust biomarkers for Parkinson disease (PD) is currently hampered by inherent technical limitations associated with imaging or antibody-based protein assays. To circumvent the challenges, we adapted a staged pipeline, starting from our previous proteomic profiling followed by high-throughput targeted mass spectrometry (MS), to identify peptides in human cerebrospinal fluid (CSF) for PD diagnosis and disease severity correlation. In this multicenter study consisting of training and validation sets, a total of 178 subjects were randomly selected from a retrospective cohort, matching age and sex between PD patients, healthy controls, and neurological controls with Alzheimer disease (AD). From ∼14,000 unique peptides displaying differences between PD and healthy control in proteomic investigations, 126 peptides were selected based on relevance and observability in CSF using bioinformatic analysis and MS screening, and then quantified by highly accurate and sensitive selected reaction monitoring (SRM) in the CSF of 30 PD patients versus 30 healthy controls (training set), followed by diagnostic (receiver operating characteristics) and disease severity correlation analyses. The most promising candidates were further tested in an independent cohort of 40 PD patients, 38 AD patients, and 40 healthy controls (validation set). A panel of five peptides (derived from SPP1, LRP1, CSF1R, EPHA4, and TIMP1) was identified to provide an area under curve (AUC) of 0.873 (sensitivity = 76.7%, specificity = 80.0%) for PD versus healthy controls in the training set. The performance was essentially confirmed in the validation set (AUC = 0.853, sensitivity = 82.5%, specificity = 82.5%). Additionally, this panel could also differentiate the PD and AD groups (AUC = 0.990, sensitivity = 95.0%, specificity = 97.4%). Furthermore, a combination of two peptides belonging to proteins TIMP1 and APLP1 significantly correlated with disease severity as determined by the Unified Parkinson's Disease Rating Scale motor scores in both the training (r = 0.381, p = 0.038)j and the validation (r = 0.339, p = 0.032) sets. The novel panel of CSF peptides, if validated in independent cohorts, could be used to assist in clinical diagnosis of PD and has the potential to help monitoring or predicting disease progression.
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Affiliation(s)
- Min Shi
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - James Movius
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Romel Dator
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Patrick Aro
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Yanchun Zhao
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Catherine Pan
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Xiangmin Lin
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104; §School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Theo K Bammler
- ¶Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195
| | - Tessandra Stewart
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104
| | - Cyrus P Zabetian
- ‖Geriatric and Parkinson's Disease Research, Education, and Clinical Centers, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108; **Department of Neurology, University of Washington School of Medicine, Seattle, Washington 98195
| | - Elaine R Peskind
- ‡‡Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington 98195; §§Mental Illness Research, Education, and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108
| | - Shu-Ching Hu
- ‖Geriatric and Parkinson's Disease Research, Education, and Clinical Centers, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108; **Department of Neurology, University of Washington School of Medicine, Seattle, Washington 98195
| | - Joseph F Quinn
- ¶¶Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
| | - Douglas R Galasko
- ‖‖Department of Neurosciences, University of California at San Diego, La Jolla, California 92093
| | - Jing Zhang
- From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;
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40
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Khristenko N, Domon B. Quantification of proteins in urine samples using targeted mass spectrometry methods. Methods Mol Biol 2015; 1243:207-220. [PMID: 25384748 DOI: 10.1007/978-1-4939-1872-0_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Numerous clinical proteomics studies are focused on the development of biomarkers to improve either diagnostics for early disease detection or the monitoring of the response to the treatment. Although, a wealth of biomarker candidates are available, their evaluation and validation in a true clinical setup remains challenging. In biomarkers evaluation studies, a panel of proteins of interest are systematically analyzed in a large cohort of samples. However, in spite of the latest progresses in mass spectrometry, the consistent detection of pertinent proteins in high complex biological samples is still a challenging task. Thus, targeted LC-MS/MS methods are better suited for the systematic analysis of biomarkers rather than shotgun approaches. This chapter describes the workflow used to perform targeted quantitative analyses of proteins in urinary samples. The peptides, as surrogates of the protein of interest, are commonly measured using a triple quadrupole mass spectrometers operated in selected reaction monitoring (SRM) mode. More recently, the advances in targeted LC-MS/MS analysis based on parallel reaction monitoring (PRM) performed on a quadrupole-orbitrap instrument have allowed to increase the specificity and selectivity of the measurements.
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Affiliation(s)
- Nina Khristenko
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, 1A-B, Rue Thomas Edison, L-1445, Strassen, Luxembourg
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41
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Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E, Brun V. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. J Proteome Res 2014; 14:787-803. [PMID: 25495225 DOI: 10.1021/pr500834z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy, and precision of peptide detection and quantification. Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS proteomic data obtained under different experimental conditions. Here, we describe the design, synthesis, and validation of a universal protein standard, called DIGESTIF, that can be added to any biological sample. The DIGESTIF standard consists of a soluble recombinant protein scaffold to which a set of 11 artificial peptides (iRT peptides) with good ionization properties has been incorporated. In the protein scaffold, the amino acids flanking iRT peptide cleavage sites were selected either to favor or hinder protease cleavage. After sample processing, the retention time and relative intensity pattern of the released iRT peptides can be used to assess the quality of sample workup, the extent of digestion, and the performance of the LC-MS system. Thus, DIGESTIF can be used to standardize a broad spectrum of applications, ranging from simple replicate measurements to large-scale biomarker screening in biomedical applications.
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42
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Pan C, Zhou Y, Dator R, Ginghina C, Zhao Y, Movius J, Peskind E, Zabetian CP, Quinn J, Galasko D, Stewart T, Shi M, Zhang J. Targeted discovery and validation of plasma biomarkers of Parkinson's disease. J Proteome Res 2014; 13:4535-45. [PMID: 24853996 PMCID: PMC4224986 DOI: 10.1021/pr500421v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite extensive research, an unmet need remains for protein biomarkers of Parkinson's disease (PD) in peripheral body fluids, especially blood, which is easily accessible clinically. The discovery of such biomarkers is challenging, however, due to the enormous complexity and huge dynamic range of human blood proteins, which are derived from nearly all organ systems, with those originating specifically from the central nervous system (CNS) being exceptionally low in abundance. In this investigation of a relatively large cohort (∼300 subjects), selected reaction monitoring (SRM) assays (a targeted approach) were used to probe plasma peptides derived from glycoproteins previously found to be altered in the CNS based on PD diagnosis or severity. Next, the detected peptides were interrogated for their diagnostic sensitivity and specificity as well as the correlation with PD severity, as determined by the Unified Parkinson's Disease Rating Scale (UPDRS). The results revealed that 12 of the 50 candidate glycopeptides were reliably and consistently identified in plasma samples, with three of them displaying significant differences among diagnostic groups. A combination of four peptides (derived from PRNP, HSPG2, MEGF8, and NCAM1) provided an overall area under curve (AUC) of 0.753 (sensitivity: 90.4%; specificity: 50.0%). Additionally, combining two peptides (derived from MEGF8 and ICAM1) yielded significant correlation with PD severity, that is, UPDRS (r = 0.293, p = 0.004). The significance of these results is at least two-fold: (1) it is possible to use a targeted approach to identify otherwise very difficult to detect CNS related biomarkers in peripheral blood and (2) the novel biomarkers, if validated in independent cohorts, can be employed to assist with clinical diagnosis of PD as well as monitoring disease progression.
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Affiliation(s)
- Catherine Pan
- Department of Pathology, University of Washington School of Medicine , 325 9th Avenue, HMC 359635, Seattle, Washington 98104, United States
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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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Kume H, Muraoka S, Kuga T, Adachi J, Narumi R, Watanabe S, Kuwano M, Kodera Y, Matsushita K, Fukuoka J, Masuda T, Ishihama Y, Matsubara H, Nomura F, Tomonaga T. Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis. Mol Cell Proteomics 2014; 13:1471-84. [PMID: 24687888 DOI: 10.1074/mcp.m113.037093] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851.
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Affiliation(s)
- Hideaki Kume
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Satoshi Muraoka
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Takahisa Kuga
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Jun Adachi
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Ryohei Narumi
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Shio Watanabe
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Masayoshi Kuwano
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Yoshio Kodera
- §Laboratory of Biomolecular Dynamics, Department of Physics, Kitasato University School of Science, Kanagawa, Japan
| | - Kazuyuki Matsushita
- ¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Junya Fukuoka
- **Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Masuda
- ‡‡Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Yasushi Ishihama
- §§Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hisahiro Matsubara
- ¶¶Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumio Nomura
- ¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Takeshi Tomonaga
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
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45
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Liu Y, Hüttenhain R, Collins B, Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev Mol Diagn 2013; 13:811-25. [PMID: 24138574 PMCID: PMC3833812 DOI: 10.1586/14737159.2013.845089] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Among the wide range of proteomic technologies, targeted mass spectrometry (MS) has shown great potential for biomarker studies. To extend the degree of multiplexing achieved by selected reaction monitoring (SRM), we recently developed SWATH MS. SWATH MS is a variant of the emerging class of data-independent acquisition (DIA) methods and essentially converts the molecules in a physical sample into perpetually re-usable digital maps. The thus generated SWATH maps are then mined using a targeted data extraction strategy, allowing us to profile disease-related proteomes at a high degree of reproducibility. The successful application of both SRM and SWATH MS requires the a priori generation of reference spectral maps that provide coordinates for quantification. Herein, we demonstrate that the application of the mass spectrometric reference maps and the acquisition of personalized SWATH maps hold a particular promise for accelerating the current process of biomarker discovery.
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Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str.16, 8093 Zurich, Switzerland
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Végvári Á, Sjödin K, Rezeli M, Malm J, Lilja H, Laurell T, Marko-Varga G. Identification of a novel proteoform of prostate specific antigen (SNP-L132I) in clinical samples by multiple reaction monitoring. Mol Cell Proteomics 2013; 12:2761-73. [PMID: 23842001 PMCID: PMC3790289 DOI: 10.1074/mcp.m113.028365] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/07/2013] [Indexed: 12/12/2022] Open
Abstract
Prostate specific antigen (PSA) is a well-established tumor marker that is frequently employed as model biomarker in the development and evaluation of emerging quantitative proteomics techniques, partially as a result of wide access to commercialized immunoassays serving as "gold standards." We designed a multiple reaction monitoring (MRM) assay to detect PSA proteoforms in clinical samples (n = 72), utilizing the specificity and sensitivity of the method. We report, for the first time, a PSA proteoform coded by SNP-L132I (rs2003783) that was observed in nine samples in both heterozygous (n = 7) and homozygous (n = 2) expression profiles. Other isoforms of PSA, derived from protein databases, were not identified by four unique proteotypic tryptic peptides. We have also utilized our MRM assay for precise quantitative analysis of PSA concentrations in both seminal and blood plasma samples. The analytical performance was evaluated, and close agreement was noted between quantitations based on three selected peptides (LSEPAELTDAVK, IVGGWECEK, and SVILLGR) and a routinely used commercialized immunoassay. Additionally, we disclose that the peptide IVGGWECEK is shared with kallikrein-related peptidase 2 and therefore is not unique for PSA. Thus, we propose the use of another tryptic sequence (SVILLGR) for accurate MRM quantification of PSA in clinical samples.
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Affiliation(s)
- Ákos Végvári
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Karin Sjödin
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Melinda Rezeli
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Johan Malm
- ¶Dept. of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, SE-205 02 Malmö, Sweden
| | - Hans Lilja
- ¶Dept. of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, SE-205 02 Malmö, Sweden
- ‖Depts. of Laboratory Medicine, Surgery (Urology), and Medicine (GU-Oncology), Memorial Sloan-Kettering Cancer Center, New York, New York 10065
- **Nuffield Dept. of Surgical Sciences, University of Oxford, Oxford, OX3 9DU UK
- ‡‡Institute of Biomedical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland
| | - Thomas Laurell
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- §§Dept. of Biomedical Engineering, Dongguk University, Seoul, 100-715, South Korea
| | - György Marko-Varga
- From ‡Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- ¶¶First Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, 160-0023 Japan
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47
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Jeudy J, Salvador A, Simon R, Jaffuel A, Fonbonne C, Léonard JF, Gautier JC, Pasquier O, Lemoine J. Overcoming biofluid protein complexity during targeted mass spectrometry detection and quantification of protein biomarkers by MRM cubed (MRM3). Anal Bioanal Chem 2013; 406:1193-200. [DOI: 10.1007/s00216-013-7266-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/02/2013] [Accepted: 07/17/2013] [Indexed: 01/19/2023]
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48
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Optimization of liquid chromatography–multiple reaction monitoring cubed mass spectrometry assay for protein quantification: Application to aquaporin-2 water channel in human urine. J Chromatogr A 2013; 1301:122-30. [DOI: 10.1016/j.chroma.2013.05.068] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/28/2013] [Accepted: 05/28/2013] [Indexed: 12/13/2022]
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49
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Kim Y, Kislinger T. Novel approaches for the identification of biomarkers of aggressive prostate cancer. Genome Med 2013; 5:56. [PMID: 23809668 PMCID: PMC3706951 DOI: 10.1186/gm460] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ability to distinguish indolent from aggressive prostate tumors remains one of the greatest challenges in the management of this disease. Ongoing efforts to establish a panel of molecular signatures, comprising gene expression profiles, proteins, epigenetic patterns, or a combination of these alterations, are being propelled by rapid advancements in 'omics' technologies. The identification of such biomarkers in biological fluids is an especially attractive goal for clinical applications. Here, we summarize recent progress in the identification of candidate prognostic biomarkers of prostate cancer using biological fluid samples.
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Affiliation(s)
- Yunee Kim
- Department of Medical Biophysics, University of Toronto, Toronto, Canada M5G 1L7
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada M5G 1L7 ; Princess Margaret Cancer Center, University Health Network, Toronto, Canada M5G 1L7
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50
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Demartini DR, Pasquali G, Carlini CR. An overview of proteomics approaches applied to biopharmaceuticals and cyclotides research. J Proteomics 2013; 93:224-33. [PMID: 23777896 DOI: 10.1016/j.jprot.2013.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/03/2013] [Accepted: 06/06/2013] [Indexed: 01/22/2023]
Abstract
The evolution in proteomics approaches is notable, including quantitative proteomics and strategies for elucidation of post-translational modifications. Faster and more accurate mass spectrometers as well as cleverer bioinformatics tolls are making the difference in such advancement. Among the wide range of research in plant proteomics, biopharmaceutical production using plants as "biofactories" and the screening of new activities of new molecules, in this case, peptides, are quite important regarding translational proteomics. The present review is focused on "recombinant proteins and bioactive peptides", with biopharmaceuticals and cyclotides chosen as examples. Their application and challenges are focused on a "translational proteomics" point of view, in order to exemplify some new areas of research based on proteomics strategies. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Diogo Ribeiro Demartini
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul., Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, Porto Alegre, RS 91501-970, Brazil.
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