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Richard V, Mitsa G, Eshghi A, Chaplygina D, Mohammed Y, Goodlett DR, Zahedi RP, Thevis M, Borchers CH. Establishing Personalized Blood Protein Reference Ranges Using Noninvasive Microsampling and Targeted Proteomics: Implications for Antidoping Strategies. J Proteome Res 2024; 23:1779-1787. [PMID: 38655860 PMCID: PMC11077581 DOI: 10.1021/acs.jproteome.4c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
To prevent doping practices in sports, the World Anti-Doping Agency implemented the Athlete Biological Passport (ABP) program, monitoring biological variables over time to indirectly reveal the effects of doping rather than detect the doping substance or the method itself. In the context of this program, a highly multiplexed mass spectrometry-based proteomics assay for 319 peptides corresponding to 250 proteins was developed, including proteins associated with blood-doping practices. "Baseline" expression profiles of these potential biomarkers in capillary blood (dried blood spots (DBS)) were established using multiple reaction monitoring (MRM). Combining DBS microsampling with highly multiplexed MRM assays is the best-suited technology to enhance the effectiveness of the ABP program, as it represents a cost-effective and robust alternative analytical method with high specificity and selectivity of targets in the attomole range. DBS data were collected from 10 healthy athlete volunteers over a period of 140 days (28 time points per participant). These comprehensive findings provide a personalized targeted blood proteome "fingerprint" showcasing that the targeted proteome is unique to an individual and likely comparable to a DNA fingerprint. The results can serve as a baseline for future studies investigating doping-related perturbations.
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Affiliation(s)
- Vincent
R. Richard
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Georgia Mitsa
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Division
of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1, Canada
| | - Azad Eshghi
- University
of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada
| | - Daria Chaplygina
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZC, The Netherlands
| | - David R. Goodlett
- University
of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada
| | - Rene P. Zahedi
- Manitoba
Centre for Proteomics and Systems Biology, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Biochemistry and Medical Genetics, University
of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- CancerCare
Manitoba Research Institute, Winnipeg, Manitoba R3E 0V9, Canada
| | - Mario Thevis
- Institute
of Biochemistry, Center for Preventive Doping Research, German Sport University Cologne, Cologne 50933, Germany
- European
Monitoring Center for Emerging Doping Agents (EuMoCEDA), Cologne/Bonn 50933, Germany
| | - Christoph H. Borchers
- Segal
Cancer Proteomics Centre, Lady Davis Institute
for Medical Research, Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Division
of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1, Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montréal, Quebec H4A 3T2, Canada
- Department
of Pathology, McGill University, Montréal, Quebec H4A 3J1, Canada
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2
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Huang CF, Kline JT, Negrão F, Robey MT, Toby TK, Durbin KR, Fellers RT, Friedewald JJ, Levitsky J, Abecassis MMI, Melani RD, Kelleher NL, Fornelli L. Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring. Anal Chem 2024; 96:3578-3586. [PMID: 38354049 PMCID: PMC11008684 DOI: 10.1021/acs.analchem.3c05578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Existing mass spectrometric assays used for sensitive and specific measurements of target proteins across multiple samples, such as selected/multiple reaction monitoring (SRM/MRM) or parallel reaction monitoring (PRM), are peptide-based methods for bottom-up proteomics. Here, we describe an approach based on the principle of PRM for the measurement of intact proteoforms by targeted top-down proteomics, termed proteoform reaction monitoring (PfRM). We explore the ability of our method to circumvent traditional limitations of top-down proteomics, such as sensitivity and reproducibility. We also introduce a new software program, Proteoform Finder (part of ProSight Native), specifically designed for the easy analysis of PfRM data. PfRM was initially benchmarked by quantifying three standard proteins. The linearity of the assay was shown over almost 3 orders of magnitude in the femtomole range, with limits of detection and quantification in the low femtomolar range. We later applied our multiplexed PfRM assay to complex samples to quantify biomarker candidates in peripheral blood mononuclear cells (PBMCs) from liver-transplanted patients, suggesting their possible translational applications. These results demonstrate that PfRM has the potential to contribute to the accurate quantification of protein biomarkers for diagnostic purposes and to improve our understanding of disease etiology at the proteoform level.
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Affiliation(s)
- Che-Fan Huang
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Jake T Kline
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Fernanda Negrão
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew T Robey
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - Timothy K Toby
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Kenneth R Durbin
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - Ryan T Fellers
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - John J Friedewald
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Josh Levitsky
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Michael M I Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Luca Fornelli
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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3
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Mohammed Y, Tran K, Carlsten C, Ryerson C, Wong A, Lee T, Cheng MP, Vinh DC, Lee TC, Winston BW, Sweet D, Boyd JH, Walley KR, Haljan G, McGeer A, Lamontagne F, Fowler R, Maslove D, Singer J, Patrick DM, Marshall JC, Murthy S, Jain F, Borchers CH, Goodlett DR, Levin A, Russell JA. Proteomic Evolution from Acute to Post-COVID-19 Conditions. J Proteome Res 2024; 23:52-70. [PMID: 38048423 PMCID: PMC10775146 DOI: 10.1021/acs.jproteome.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 11/13/2023] [Indexed: 12/06/2023]
Abstract
Many COVID-19 survivors have post-COVID-19 conditions, and females are at a higher risk. We sought to determine (1) how protein levels change from acute to post-COVID-19 conditions, (2) whether females have a plasma protein signature different from that of males, and (3) which biological pathways are associated with COVID-19 when compared to restrictive lung disease. We measured protein levels in 74 patients on the day of admission and at 3 and 6 months after diagnosis. We determined protein concentrations by multiple reaction monitoring (MRM) using a panel of 269 heavy-labeled peptides. The predicted forced vital capacity (FVC) and diffusing capacity of the lungs for carbon monoxide (DLCO) were measured by routine pulmonary function testing. Proteins associated with six key lipid-related pathways increased from admission to 3 and 6 months; conversely, proteins related to innate immune responses and vasoconstriction-related proteins decreased. Multiple biological functions were regulated differentially between females and males. Concentrations of eight proteins were associated with FVC, %, and they together had c-statistics of 0.751 (CI:0.732-0.779); similarly, concentrations of five proteins had c-statistics of 0.707 (CI:0.676-0.737) for DLCO, %. Lipid biology may drive evolution from acute to post-COVID-19 conditions, while activation of innate immunity and vascular regulation pathways decreased over that period. (ProteomeXchange identifiers: PXD041762, PXD029437).
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Affiliation(s)
- Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
- UVic-Genome
BC Proteomics Centre, University of Victoria, Victoria V8Z 5N3, BC Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montreal, QC H3A 0G4, Canada
| | - Karen Tran
- Division
of General Internal Medicine, Vancouver
General Hospital and University of British Columbia, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
| | - Chris Carlsten
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Christopher Ryerson
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Alyson Wong
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Terry Lee
- Centre for
Health Evaluation and Outcome Science (CHEOS), St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Matthew P. Cheng
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
| | - Donald C. Vinh
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
| | - Todd C. Lee
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
| | - Brent W. Winston
- Departments
of Critical Care Medicine, Medicine and Biochemistry and Molecular
Biology, Foothills Medical Centre and University
of Calgary, 1403 29 Street
NW, Calgary, Alberta T2N 4N1, Canada
| | - David Sweet
- Division
of Critical Care Medicine, Vancouver General
Hospital, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
| | - John H. Boyd
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Keith R. Walley
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Greg Haljan
- Department of Medicine, Surrey Memorial
Hospital, 13750 96th
Avenue, Surrey, BC V3V 1Z2, Canada
| | - Allison McGeer
- Mt. Sinai Hospital and University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | | | - Robert Fowler
- Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | - David Maslove
- Department
of Critical Care, Kingston General Hospital
and Queen’s University, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
| | - Joel Singer
- Centre for
Health Evaluation and Outcome Science (CHEOS), St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - David M. Patrick
- British Columbia Centre for Disease Control
(BCCDC) and University
of British Columbia, 655 West 12th Avenue, Vancouver, BC V5Z 4R4, Canada
| | - John C. Marshall
- Department of Surgery, St. Michael’s
Hospital, 30 Bond Street, Toronto, ON M5B
1W8, Canada
| | - Srinivas Murthy
- BC Children’s Hospital and University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Fagun Jain
- Black Tusk Research Group, Vancouver, BC V6Z 2C7, Canada
| | - Christoph H. Borchers
- Segal Cancer Proteomics, Centre, Lady Davis
Institute
for Medical Research, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Division of Experimental Medicine, McGill
University, Montreal, QC H3T 1E2, Canada
- Department of Pathology, McGill
University, Montreal, QC H3T 1E2, Canada
| | - David R. Goodlett
- UVic-Genome
BC Proteomics Centre, University of Victoria, Victoria V8Z 5N3, BC Canada
| | - Adeera Levin
- Division of Nephrology, St.
Paul’s Hospital, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - James A. Russell
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - ARBs CORONA I Consortium
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
- UVic-Genome
BC Proteomics Centre, University of Victoria, Victoria V8Z 5N3, BC Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montreal, QC H3A 0G4, Canada
- Division
of General Internal Medicine, Vancouver
General Hospital and University of British Columbia, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Centre for
Health Evaluation and Outcome Science (CHEOS), St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
- Departments
of Critical Care Medicine, Medicine and Biochemistry and Molecular
Biology, Foothills Medical Centre and University
of Calgary, 1403 29 Street
NW, Calgary, Alberta T2N 4N1, Canada
- Division
of Critical Care Medicine, Vancouver General
Hospital, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Department of Medicine, Surrey Memorial
Hospital, 13750 96th
Avenue, Surrey, BC V3V 1Z2, Canada
- Mt. Sinai Hospital and University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
- University of Sherbrooke, Sherbrooke, PQ J1K 2R1, Canada
- Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
- Department
of Critical Care, Kingston General Hospital
and Queen’s University, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
- British Columbia Centre for Disease Control
(BCCDC) and University
of British Columbia, 655 West 12th Avenue, Vancouver, BC V5Z 4R4, Canada
- Department of Surgery, St. Michael’s
Hospital, 30 Bond Street, Toronto, ON M5B
1W8, Canada
- BC Children’s Hospital and University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- Black Tusk Research Group, Vancouver, BC V6Z 2C7, Canada
- Segal Cancer Proteomics, Centre, Lady Davis
Institute
for Medical Research, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Division of Experimental Medicine, McGill
University, Montreal, QC H3T 1E2, Canada
- Department of Pathology, McGill
University, Montreal, QC H3T 1E2, Canada
- Division of Nephrology, St.
Paul’s Hospital, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
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Mehta K, Mohebbi M, Pasco JA, Williams LJ, Sui SX, Walder K, Ng BL, Gupta VB. A plasma protein signature associated with cognitive function in men without severe cognitive impairment. Alzheimers Res Ther 2023; 15:148. [PMID: 37658429 PMCID: PMC10472730 DOI: 10.1186/s13195-023-01294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND A minimally invasive blood-based assessment of cognitive function could be a promising screening strategy to identify high-risk groups for the incidence of Alzheimer's disease. METHODS The study included 448 cognitively unimpaired men (mean age 64.1 years) drawn from the Geelong Osteoporosis Study. A targeted mass spectrometry-based proteomic assay was performed to measure the abundance levels of 269 plasma proteins followed by linear regression analyses adjusted for age and APOE ε4 carrier status to identify the biomarkers related to overall cognitive function. Furthermore, two-way interactions were conducted to see whether Alzheimer's disease-linked genetic variants or health conditions modify the association between biomarkers and cognitive function. RESULTS Ten plasma proteins showed an association with overall cognitive function. This association was modified by allelic variants in genes ABCA7, CLU, BDNF and MS4A6A that have been previously linked to Alzheimer's disease. Modifiable health conditions such as mood disorders and poor bone health, which are postulated to be risk factors for Alzheimer's disease, also impacted the relationship observed between protein marker levels and cognition. In addition to the univariate analyses, an 11-feature multianalyte model was created using the least absolute shrinkage and selection operator regression that identified 10 protein features and age associated with cognitive function. CONCLUSIONS Overall, the present study revealed plasma protein candidates that may contribute to the development of a blood-based screening test for identifying early cognitive changes. This study also highlights the importance of considering other risk factors in elucidating the relationship between biomarkers and cognition, an area that remains largely unexplored.
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Affiliation(s)
- Kanika Mehta
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Mohammadreza Mohebbi
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Biostatistics Unit, Faculty of Health, Deakin University, Burwood, VIC, Australia
| | - Julie A Pasco
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Department of Medicine-Western Health, The University of Melbourne, St Albans, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Prahran, VIC, Australia
- Barwon Health, Geelong, VIC, Australia
| | - Lana J Williams
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Barwon Health, Geelong, VIC, Australia
| | - Sophia X Sui
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
| | - Ken Walder
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
| | - Boon Lung Ng
- Department of Geriatric Medicine, Barwon Health, Geelong, VIC, Australia
| | - Veer Bala Gupta
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia.
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Kononikhin AS, Brzhozovskiy AG, Bugrova AE, Chebotareva NV, Zakharova NV, Semenov S, Vinogradov A, Indeykina MI, Moiseev S, Larina IM, Nikolaev EN. Targeted MRM Quantification of Urinary Proteins in Chronic Kidney Disease Caused by Glomerulopathies. Molecules 2023; 28:molecules28083323. [PMID: 37110557 PMCID: PMC10142111 DOI: 10.3390/molecules28083323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/28/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Glomerulopathies with nephrotic syndrome that are resistant to therapy often progress to end-stage chronic kidney disease (CKD) and require timely and accurate diagnosis. Targeted quantitative urine proteome analysis by mass spectrometry (MS) with multiple-reaction monitoring (MRM) is a promising tool for early CKD diagnostics that could replace the invasive biopsy procedure. However, there are few studies regarding the development of highly multiplexed MRM assays for urine proteome analysis, and the two MRM assays for urine proteomics described so far demonstrate very low consistency. Thus, the further development of targeted urine proteome assays for CKD is actual task. Herein, a BAK270 MRM assay previously validated for blood plasma protein analysis was adapted for urine-targeted proteomics. Because proteinuria associated with renal impairment is usually associated with an increased diversity of plasma proteins being present in urine, the use of this panel was appropriate. Another advantage of the BAK270 MRM assay is that it includes 35 potential CKD markers described previously. Targeted LC-MRM MS analysis was performed for 69 urine samples from 46 CKD patients and 23 healthy controls, revealing 138 proteins that were found in ≥2/3 of the samples from at least one of the groups. The results obtained confirm 31 previously proposed CKD markers. Combination of MRM analysis with machine learning for data processing was performed. As a result, a highly accurate classifier was developed (AUC = 0.99) that enables distinguishing between mild and severe glomerulopathies based on the assessment of only three urine proteins (GPX3, PLMN, and A1AT or SHBG).
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Affiliation(s)
- Alexey S Kononikhin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Alexander G Brzhozovskiy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of the Ministry of Health, 117997 Moscow, Russia
| | - Anna E Bugrova
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of the Ministry of Health, 117997 Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Kosygina Str. 4, 119334 Moscow, Russia
| | - Natalia V Chebotareva
- Nephrology Department, Sechenov First Moscow State Medical University, Trubezkaya 8, 119048 Moscow, Russia
- Department of Internal Medicine, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Natalia V Zakharova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Kosygina Str. 4, 119334 Moscow, Russia
| | - Savva Semenov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Anatoliy Vinogradov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Internal Medicine, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Maria I Indeykina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Kosygina Str. 4, 119334 Moscow, Russia
| | - Sergey Moiseev
- Nephrology Department, Sechenov First Moscow State Medical University, Trubezkaya 8, 119048 Moscow, Russia
| | - Irina M Larina
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, Khoroshevskoe Shosse 76A, 123007 Moscow, Russia
| | - Evgeny N Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
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6
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Kalinskaya A, Vorobyeva D, Rusakovich G, Maryukhnich E, Anisimova A, Dukhin O, Elizarova A, Ivanova O, Bugrova A, Brzhozovskiy A, Kononikhin A, Nikolaev E, Vasilieva E. Targeted Blood Plasma Proteomics and Hemostasis Assessment of Post COVID-19 Patients with Acute Myocardial Infarction. Int J Mol Sci 2023; 24:ijms24076523. [PMID: 37047497 PMCID: PMC10094800 DOI: 10.3390/ijms24076523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The molecular mechanisms underlying cardiovascular complications after the SARS-CoV-2 infection remain unknown. The goal of our study was to analyze the features of blood coagulation, platelet aggregation, and plasma proteomics in COVID-19 convalescents with AMI. The study included 66 AMI patients and 58 healthy volunteers. The groups were divided according to the anti-N IgG levels (AMI post-COVID (n = 44), AMI control (n = 22), control post-COVID (n = 31), and control (n = 27)). All participants underwent rotational thromboelastometry, thrombodynamics, impedance aggregometry, and blood plasma proteomics analysis. Both AMI groups of patients demonstrated higher values of clot growth rates, thrombus size and density, as well as the elevated levels of components of the complement system, proteins modifying the state of endothelium, acute-phase and procoagulant proteins. In comparison with AMI control, AMI post-COVID patients demonstrated decreased levels of proteins connected to inflammation and hemostasis (lipopolysaccharide-binding protein, C4b-binding protein alpha-chain, plasma protease C1 inhibitor, fibrinogen beta-chain, vitamin K-dependent protein S), and altered correlations between inflammation and fibrinolysis. A new finding is that AMI post-COVID patients opposite the AMI control group, are characterized by a less noticeable growth of acute-phase proteins and hemostatic markers that could be explained by prolonged immune system alteration after COVID-19.
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7
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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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8
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Kliuchnikova AA, Novikova SE, Ilgisonis EV, Kiseleva OI, Poverennaya EV, Zgoda VG, Moshkovskii SA, Poroikov VV, Lisitsa AV, Archakov AI, Ponomarenko EA. Blood Plasma Proteome: A Meta-Analysis of the Results of Protein Quantification in Human Blood by Targeted Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24010769. [PMID: 36614211 PMCID: PMC9821253 DOI: 10.3390/ijms24010769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
A meta-analysis of the results of targeted quantitative screening of human blood plasma was performed to generate a reference standard kit that can be used for health analytics. The panel included 53 of the 296 proteins that form a “stable” part of the proteome of a healthy individual; these proteins were found in at least 70% of samples and were characterized by an interindividual coefficient of variation <40%. The concentration range of the selected proteins was 10−10−10−3 M and enrichment analysis revealed their association with rare familial diseases. The concentration of ceruloplasmin was reduced by approximately three orders of magnitude in patients with neurological disorders compared to healthy volunteers, and those of gelsolin isoform 1 and complement factor H were abruptly reduced in patients with lung adenocarcinoma. Absolute quantitative data of the individual proteome of a healthy and diseased individual can be used as the basis for personalized medicine and health monitoring. Storage over time allows us to identify individual biomarkers in the molecular landscape and prevent pathological conditions.
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Affiliation(s)
- Anna A. Kliuchnikova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | | | | | | | | | | | - Sergei A. Moshkovskii
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Department of Biochemistry, Medico-Biological Faculty, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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9
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Caron NS, Haqqani AS, Sandhu A, Aly AE, Findlay Black H, Bone JN, McBride JL, Abulrob A, Stanimirovic D, Leavitt BR, Hayden MR. Cerebrospinal fluid biomarkers for assessing Huntington disease onset and severity. Brain Commun 2022; 4:fcac309. [PMID: 36523269 PMCID: PMC9746690 DOI: 10.1093/braincomms/fcac309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/02/2022] [Accepted: 11/23/2022] [Indexed: 08/27/2023] Open
Abstract
The identification of molecular biomarkers in CSF from individuals affected by Huntington disease may help improve predictions of disease onset, better define disease progression and could facilitate the evaluation of potential therapies. The primary objective of our study was to investigate novel CSF protein candidates and replicate previously reported protein biomarker changes in CSF from Huntington disease mutation carriers and healthy controls. Our secondary objective was to compare the discriminatory potential of individual protein analytes and combinations of CSF protein markers for stratifying individuals based on the severity of Huntington disease. We conducted a hypothesis-driven analysis of 26 pre-specified protein analytes in CSF from 16 manifest Huntington disease subjects, eight premanifest Huntington disease mutation carriers and eight healthy control individuals using parallel-reaction monitoring mass spectrometry. In addition to reproducing reported changes in previously investigated CSF biomarkers (NEFL, PDYN, and PENK), we also identified novel exploratory CSF proteins (C1QB, CNR1, GNAL, IDO1, IGF2, and PPP1R1B) whose levels were altered in Huntington disease mutation carriers and/or across stages of disease. Moreover, we report strong associations of select CSF proteins with clinical measures of disease severity in manifest Huntington disease subjects (C1QB, CNR1, NEFL, PDYN, PPP1R1B, and TTR) and with years to predicted disease onset in premanifest Huntington disease mutation carriers (ALB, C4B, CTSD, IGHG1, and TTR). Using receiver operating characteristic curve analysis, we identified PENK as being the most discriminant CSF protein for stratifying Huntington disease mutation carriers from controls. We also identified exploratory multi-marker CSF protein panels that improved discrimination of premanifest Huntington disease mutation carriers from controls (PENK, ALB and NEFL), early/mid-stage Huntington disease from premanifest mutation carriers (PPP1R1B, TTR, CHI3L1, and CTSD), and late-stage from early/mid-stage Huntington disease (CNR1, PPP1R1B, BDNF, APOE, and IGHG1) compared with individual CSF proteins. In this study, we demonstrate that combinations of CSF proteins can outperform individual markers for stratifying individuals based on Huntington disease mutation status and disease severity. Moreover, we define exploratory multi-marker CSF protein panels that, if validated, may be used to improve the accuracy of disease-onset predictions, complement existing clinical and imaging biomarkers for monitoring the severity of Huntington disease, and potentially for assessing therapeutic response in clinical trials. Additional studies with CSF collected from larger cohorts of Huntington disease mutation carriers are needed to replicate these exploratory findings.
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Affiliation(s)
- Nicholas S Caron
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Arsalan S Haqqani
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
| | - Akshdeep Sandhu
- BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Amirah E Aly
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Hailey Findlay Black
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Jeffrey N Bone
- BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Jodi L McBride
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Abedelnasser Abulrob
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
| | - Danica Stanimirovic
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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10
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Zakharova NV, Bugrova AE, Indeykina MI, Fedorova YB, Kolykhalov IV, Gavrilova SI, Nikolaev EN, Kononikhin AS. Proteomic Markers and Early Prediction of Alzheimer's Disease. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:762-776. [PMID: 36171657 DOI: 10.1134/s0006297922080089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 06/16/2023]
Abstract
Alzheimer's disease (AD) is the most common socially significant neurodegenerative pathology, which currently affects more than 30 million elderly people worldwide. Since the number of patients grows every year and may exceed 115 million by 2050, and due to the lack of effective therapies, early prediction of AD remains a global challenge, solution of which can contribute to the timely appointment of a preventive therapy in order to avoid irreversible changes in the brain. To date, clinical assays for the markers of amyloidosis in cerebrospinal fluid (CSF) have been developed, which, in conjunction with the brain MRI and PET studies, are used either to confirm the diagnosis based on obligate clinical criteria or to predict the risk of AD developing at the stage of mild cognitive impairment (MCI). However, the problem of predicting AD at the asymptomatic stage remains unresolved. In this regard, the search for new protein markers and studies of proteomic changes in CSF and blood plasma are of particular interest and may consequentially identify particular pathways involved in the pathogenesis of AD. Studies of specific proteomic changes in blood plasma deserve special attention and are of increasing interest due to the much less invasive method of sample collection as compared to CSF, which is important when choosing the object for large-scale screening. This review briefly summarizes the current knowledge on proteomic markers of AD and considers the prospects of developing reliable methods for early identification of AD risk factors based on the proteomic profile.
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Affiliation(s)
- Natalia V Zakharova
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Anna E Bugrova
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Maria I Indeykina
- Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | | | | | | | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
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11
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Prognosis of Alzheimer’s Disease Using Quantitative Mass Spectrometry of Human Blood Plasma Proteins and Machine Learning. Int J Mol Sci 2022; 23:ijms23147907. [PMID: 35887259 PMCID: PMC9318764 DOI: 10.3390/ijms23147907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 12/16/2022] Open
Abstract
Early recognition of the risk of Alzheimer’s disease (AD) onset is a global challenge that requires the development of reliable and affordable screening methods for wide-scale application. Proteomic studies of blood plasma are of particular relevance; however, the currently proposed differentiating markers are poorly consistent. The targeted quantitative multiple reaction monitoring (MRM) assay of the reported candidate biomarkers (CBs) can contribute to the creation of a consistent marker panel. An MRM-MS analysis of 149 nondepleted EDTA–plasma samples (MHRC, Russia) of patients with AD (n = 47), mild cognitive impairment (MCI, n = 36), vascular dementia (n = 8), frontotemporal dementia (n = 15), and an elderly control group (n = 43) was performed using the BAK 125 kit (MRM Proteomics Inc., Canada). Statistical analysis revealed a significant decrease in the levels of afamin, apolipoprotein E, biotinidase, and serum paraoxonase/arylesterase 1 associated with AD. Different training algorithms for machine learning were performed to identify the protein panels and build corresponding classifiers for the AD prognosis. Machine learning revealed 31 proteins that are important for AD differentiation and mostly include reported earlier CBs. The best-performing classifiers reached 80% accuracy, 79.4% sensitivity and 83.6% specificity and were able to assess the risk of developing AD over the next 3 years for patients with MCI. Overall, this study demonstrates the high potential of the MRM approach combined with machine learning to confirm the significance of previously identified CBs and to propose consistent protein marker panels.
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12
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Edfors F, Iglesias MJ, Butler LM, Odeberg J. Proteomics in thrombosis research. Res Pract Thromb Haemost 2022; 6:e12706. [PMID: 35494505 PMCID: PMC9039028 DOI: 10.1002/rth2.12706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
A State of the Art lecture titled “Proteomics in Thrombosis Research” was presented at the ISTH Congress in 2021. In clinical practice, there is a need for improved plasma biomarker‐based tools for diagnosis and risk prediction of venous thromboembolism (VTE). Analysis of blood, to identify plasma proteins with potential utility for such tools, could enable an individualized approach to treatment and prevention. Technological advances to study the plasma proteome on a large scale allows broad screening for the identification of novel plasma biomarkers, both by targeted and nontargeted proteomics methods. However, assay limitations need to be considered when interpreting results, with orthogonal validation required before conclusions are drawn. Here, we review and provide perspectives on the application of affinity‐ and mass spectrometry‐based methods for the identification and analysis of plasma protein biomarkers, with potential application in the field of VTE. We also provide a future perspective on discovery strategies and emerging technologies for targeted proteomics in thrombosis research. Finally, we summarize relevant new data on this topic, presented during the 2021 ISTH Congress.
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Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
| | - Lynn M. Butler
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Clinical Chemistry and Blood Coagulation Research Department of Molecular Medicine and Surgery Karolinska Institute Stockholm Sweden
- Clinical Chemistry Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
| | - Jacob Odeberg
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
- Division of Internal Medicine University Hospital of North Norway Tromsø Norway
- Coagulation Unit Department of Hematology Karolinska University Hospital Stockholm Sweden
- Department of Medicine Solna Karolinska Institute Stockholm Sweden
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13
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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14
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Ogata S, Masuda T, Ito S, Ohtsuki S. Targeted proteomics for cancer biomarker verification and validation. Cancer Biomark 2022; 33:427-436. [DOI: 10.3233/cbm-210218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Targeted proteomics is a method that measures the amount of target proteins via liquid chromatography-tandem mass spectrometry and is used to verify and validate the candidate cancer biomarker proteins. Compared with antibody-based quantification methods such as ELISA, targeted proteomics enables rapid method development, simultaneous measurement of multiple proteins, and high-specificity detection of modifications. Moreover, by spiking the internal standard peptide, targeted proteomics detects the absolute amounts of marker proteins, which is essential for determining the cut-off values for diagnosis and thus for multi-institutional validation. With these unique features, targeted proteomics can seamlessly transfer cancer biomarker candidate proteins from the discovery phase to the verification and validation phases, thereby resulting in an accelerated cancer biomarker pipeline. Furthermore, understanding the basic principles, advantages, and disadvantages is necessary to effectively utilize targeted proteomics in cancer biomarker pipelines. This review aimed to introduce the technical principles of targeted proteomics for cancer biomarker verification and validation.
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Affiliation(s)
- Seiryo Ogata
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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15
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Mohammed Y, Goodlett DR, Cheng MP, Vinh DC, Lee TC, Mcgeer A, Sweet D, Tran K, Lee T, Murthy S, Boyd JH, Singer J, Walley KR, Patrick DM, Quan C, Ismail S, Amar L, Pal A, Bassawon R, Fesdekjian L, Gou K, Lamontagne F, Marshall J, Haljan G, Fowler R, Winston BW, Russell JA. Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19. J Proteome Res 2022; 21:975-992. [PMID: 35143212 PMCID: PMC8864781 DOI: 10.1021/acs.jproteome.1c00863] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 12/15/2022]
Abstract
The host response to COVID-19 pathophysiology over the first few days of infection remains largely unclear, especially the mechanisms in the blood compartment. We report on a longitudinal proteomic analysis of acute-phase COVID-19 patients, for which we used blood plasma, multiple reaction monitoring with internal standards, and data-independent acquisition. We measured samples on admission for 49 patients, of which 21 had additional samples on days 2, 4, 7, and 14 after admission. We also measured 30 externally obtained samples from healthy individuals for comparison at baseline. The 31 proteins differentiated in abundance between acute COVID-19 patients and healthy controls belonged to acute inflammatory response, complement activation, regulation of inflammatory response, and regulation of protein activation cascade. The longitudinal analysis showed distinct profiles revealing increased levels of multiple lipid-associated functions, a rapid decrease followed by recovery for complement activation, humoral immune response, and acute inflammatory response-related proteins, and level fluctuation in the regulation of smooth muscle cell proliferation, secretory mechanisms, and platelet degranulation. Three proteins were differentiated between survivors and nonsurvivors. Finally, increased levels of fructose-bisphosphate aldolase B were determined in patients with exposure to angiotensin receptor blockers versus decreased levels in those exposed to angiotensin-converting enzyme inhibitors. Data are available via ProteomeXchange PXD029437.
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Affiliation(s)
- Yassene Mohammed
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
| | - David R. Goodlett
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
| | - Matthew P. Cheng
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Donald C. Vinh
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Todd C. Lee
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Allison Mcgeer
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
| | - David Sweet
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Karen Tran
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Terry Lee
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Srinivas Murthy
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
| | - John H. Boyd
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - Joel Singer
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Keith R. Walley
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - David M. Patrick
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
| | - Curtis Quan
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Sara Ismail
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Laetitia Amar
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Aditya Pal
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Rayhaan Bassawon
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Lara Fesdekjian
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Karine Gou
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | | | - John Marshall
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
| | - Greg Haljan
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
| | - Robert Fowler
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
| | - Brent W. Winston
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
| | - James A. Russell
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - ARBs CORONA I
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
- University of Sherbrooke,
Sherbrooke J1K 2R1, Quebec, Canada
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
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Mohammed Y, Touw CE, Nemeth B, van Adrichem RA, Borchers CH, Rosendaal FR, van Vlijmen BJ, Cannegieter SC. Targeted proteomics for evaluating risk of venous thrombosis following traumatic lower-leg injury or knee arthroscopy. J Thromb Haemost 2022; 20:684-699. [PMID: 34919779 PMCID: PMC9303526 DOI: 10.1111/jth.15623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/22/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Patients with lower-leg cast immobilization and patients undergoing knee arthroscopy have an increased risk of venous thrombosis (VT). Guidelines are ambiguous about thromboprophylaxis use, and individual risk factors for developing VT are often ignored. To assist in VT risk stratification and guide thromboprophylaxis use, various prediction models have been developed. These models depend largely on clinical factors and provide reasonably good C-statistics of around 70%. We explored using protein levels in blood plasma measured by multiplexed quantitative targeted proteomics to predict VT. Our aim was to assess whether a VT risk prediction model based on absolute plasma protein quantification is possible. METHODS We used internal standards to quantify proteins in less than 10 μl plasma. We measured 270 proteins in samples from patients scheduled for knee arthroscopy or with lower-leg cast immobilization. The two prospective POT-(K)CAST trails allow complementary views of VT signature in blood, namely pre and post trauma, respectively. From approximately 3000 patients, 31 patients developed VT who were included and matched with double the number of controls. RESULTS Top discriminating proteins between cases and controls included APOC3, APOC4, APOC2, ATRN, F13B, and F2 in knee arthroscopy patients and APOE, SERPINF2, B2M, F13B, AFM, and C1QC in patients with lower-leg cast. A logistic regression model with cross-validation resulted in C-statistics of 88.1% (95% CI: 85.7-90.6%) and 79.6% (95% CI: 77.2-82.0%) for knee arthroscopy and cast immobilization groups respectively. CONCLUSIONS Promising C-statistics merit further exploration of the value of proteomic tests for predicting VT risk upon additional validation.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenThe Netherlands
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaBritish ColumbiaCanada
| | - Carolina E. Touw
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Orthopaedic SurgeryLeiden University Medical CenterLeidenThe Netherlands
| | - Banne Nemeth
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Orthopaedic SurgeryLeiden University Medical CenterLeidenThe Netherlands
| | - Raymond A. van Adrichem
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Orthopaedic SurgeryLeiden University Medical CenterLeidenThe Netherlands
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreSegal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyJewish General Hospital, McGill UniversityMontrealQuebecCanada
- Department of Data Intensive Science and EngineeringSkolkovo Institute of Science and TechnologySkolkovo Innovation CenterMoscowRussia
| | - Frits R. Rosendaal
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Bart J. van Vlijmen
- Einthoven Laboratory for Experimental Vascular MedicineDepartment of Internal MedicineDivision of Thrombosis & HemostasisLeiden University Medical CenterLeidenThe Netherlands
| | - Suzanne C. Cannegieter
- Department of Clinical EpidemiologyLeiden University Medical CenterLeidenThe Netherlands
- Einthoven Laboratory for Experimental Vascular MedicineDepartment of Internal MedicineDivision of Thrombosis & HemostasisLeiden University Medical CenterLeidenThe Netherlands
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Gaither C, Popp R, Zahedi RP, Borchers CH. Multiple reaction monitoring-mass spectrometry enables robust quantitation of plasma proteins regardless of whole blood processing delays that may occur in the clinic. Mol Cell Proteomics 2022; 21:100212. [PMID: 35182769 PMCID: PMC9062485 DOI: 10.1016/j.mcpro.2022.100212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/24/2022] [Accepted: 02/13/2022] [Indexed: 12/23/2022] Open
Abstract
Plasma is an important biofluid for clinical research and diagnostics. In the clinic, unpredictable delays—from minutes to hours—between blood collection and plasma generation are often unavoidable. These delays can potentially lead to protein degradation and modification and might considerably affect intact protein measurement methods such as sandwich enzyme-linked immunosorbent assays that bind proteins on two epitopes to increase specificity, thus requiring largely intact protein structures. Here, we investigated, using multiple reaction monitoring mass spectrometry (MRM-MS), how delays in plasma processing affect peptide-centric “bottom-up” proteomics. We used validated assays for proteotypic peptide surrogates of 270 human proteins to analyze plasma generated after whole blood had been kept at room temperature from 0 to 40 h to mimic delays that occur in the clinic. Moreover, we evaluated the impact of different plasma-thawing conditions on MRM-based plasma protein quantitation. We demonstrate that >90% of protein concentration measurements were unaffected by the thawing procedure and by up to 40-h delayed plasma generation, reflected by relative standard deviations (RSDs) of <30%. Of the 159 MRM assays that yielded quantitative results in 60% of the measured time points, 139 enabled a stable protein quantitation (RSD <20%), 14 showed a slight variation (RSD 20–30%), and 6 appeared unstable/irreproducible (RSD > 30%). These results demonstrate the high robustness and thus the potential for MRM-based plasma-protein quantitation to be used in a clinical setting. In contrast to enzyme-linked immunosorbent assay, peptide-based MRM assays do not require intact three-dimensional protein structures for an accurate and precise quantitation of protein concentrations in the original sample. Delays in whole blood processing often cannot be avoided in the clinic. These delays might affect measurements by intact protein assays such as ELISA. The impact on LC/MRM was evaluated using validated assays to quantify 270 proteins. >95% of the measured concentrations had RSDs <30% between delays of 0 to 40 h. Protein quantitation by LC/MRM-MS is robust against pitfalls in the clinical setting.
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Affiliation(s)
| | - Robert Popp
- MRM Proteomics Inc, Montreal, Quebec, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.
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18
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Gaither C, Popp R, Borchers SP, Skarphedinsson K, Eiriksson FF, Thorsteinsdóttir M, Mohammed Y, Borchers CH. Performance Assessment of a 125 Human Plasma Peptide Mixture Stored at Room Temperature for Multiple Reaction Monitoring-Mass Spectrometry. J Proteome Res 2021; 20:4292-4302. [PMID: 34270269 DOI: 10.1021/acs.jproteome.1c00249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic peptides are a critical requirement for the development and application of targeted mass spectrometry (MS)-based assays for the quantitation of proteins from biological matrices. Transporting synthetic peptides on dry ice from one laboratory to another is costly and often difficult because of country-specific import and export regulations. Therefore, in this study, we assessed the impact of leaving a lyophilized mixture consisting of 125 peptides at room temperature for up to 20 days, and we assessed the effect on the quantitative performance of multiple reaction monitoring-MS (MRM-MS) assays. The findings suggest that there are no significant differences in the MRM-MS results for the time points assessed in this study (up to 20 days). All the calibration curves and quality control (QC) samples met the acceptance criteria for precision and accuracy (raw data are available via the public MS data repository PanoramaWeb, identifier: /MRM Proteomics/2020_BAK125_RT). The number of endogenous proteins quantifiable across five plasma samples was consistently between 87 and 99 out of 125 for all time points. Moreover, the coefficients of variation (CVs) calculated for the majority of peptide concentrations across all samples and time points were <5%. In addition, a lyophilized peptide mixture was transported from Canada to Iceland without dry ice. The results showed that there was no significant difference in the quantitative performance, with the determined concentrations of most proteins in the samples falling within 30% between the analyses performed on the same three plasma samples in Iceland and those in Canada. Overall, a comparison of the results obtained in Canada and in Iceland indicated that the peptides were stable under the conditions tested and also indicated that shipping lyophilized peptide mixtures without dry ice, but in the presence of sufficient desiccant material, could be a feasible option in cases where transport difficulties may arise or dry-ice sublimation may occur.
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Affiliation(s)
| | - Robert Popp
- MRM Proteomics Inc., Montreal, Quebec H2X 3X8, Canada
| | | | - Kjartan Skarphedinsson
- Faculty of Pharmaceutical Sciences, University of Iceland, 107 Reykjavik, Iceland.,ArcticMass Ltd., 102 Reykjavik, Iceland
| | - Finnur F Eiriksson
- Faculty of Pharmaceutical Sciences, University of Iceland, 107 Reykjavik, Iceland.,ArcticMass Ltd., 102 Reykjavik, Iceland
| | - Margrét Thorsteinsdóttir
- Faculty of Pharmaceutical Sciences, University of Iceland, 107 Reykjavik, Iceland.,ArcticMass Ltd., 102 Reykjavik, Iceland
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada.,Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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Kraaijpoel N, Mulder FI, Carrier M, van Lieshout A, Würdinger T, Best MG, van Vlijmen BJ, Mohammed Y, Jara-Palomares L, Kamphuisen PW, Di Nisio M, Ageno W, Beyer-Westendorf J, Vanassche T, Klokm FA, Otten HM, Peters MJ, Cosmi B, Wolde MT, Bossuyt PM, Büller HR, van Es N. Novel biomarkers to detect occult cancer in patients with unprovoked venous thromboembolism: Rationale and design of the PLATO-VTE study. THROMBOSIS UPDATE 2021. [DOI: 10.1016/j.tru.2020.100030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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20
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Rotello RJ, Veenstra TD. Mass Spectrometry Techniques: Principles and Practices for Quantitative Proteomics. Curr Protein Pept Sci 2020; 22:121-133. [PMID: 32957902 DOI: 10.2174/1389203721666200921153513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/26/2020] [Accepted: 06/13/2020] [Indexed: 01/05/2023]
Abstract
In the current omics-age of research, major developments have been made in technologies that attempt to survey the entire repertoire of genes, transcripts, proteins, and metabolites present within a cell. While genomics has led to a dramatic increase in our understanding of such things as disease morphology and how organisms respond to medications, it is critical to obtain information at the proteome level since proteins carry out most of the functions within the cell. The primary tool for obtaining proteome-wide information on proteins within the cell is mass spectrometry (MS). While it has historically been associated with the protein identification, developments over the past couple of decades have made MS a robust technology for protein quantitation as well. Identifying quantitative changes in proteomes is complicated by its dynamic nature and the inability of any technique to guarantee complete coverage of every protein within a proteome sample. Fortunately, the combined development of sample preparation and MS methods have made it capable of quantitatively comparing many thousands of proteins obtained from cells and organisms.
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Affiliation(s)
- Rocco J Rotello
- School of Pharmacy, Cedarville University, Cedarville, OH 45314, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH 45314, United States
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