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Kreft IC, Hoogendijk AJ, van der Zwaan C, van Alphen FPJ, Boon-Spijker M, Prinsze F, Meijer AB, de Korte D, van den Hurk K, van den Biggelaar M. Mass spectrometry-based analysis on the impact of whole blood donation on the global plasma proteome. Transfusion 2023; 63:564-573. [PMID: 36722460 DOI: 10.1111/trf.17254] [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: 10/07/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Biomonitoring may provide important insights into the impact of a whole blood donation for individual blood donors. STUDY DESIGN AND METHODS Here, we used unbiased mass spectrometry (MS)-based proteomics to assess longitudinal changes in the global plasma proteome, after a single blood donation for new and regular donors. Subsequently, we compared plasma proteomes of 76 male and female whole blood donors, that were grouped based on their ferritin and hemoglobin (Hb) levels. RESULTS The longitudinal analysis showed limited changes in the plasma proteomes of new and regular donors after a whole blood donation during a 180-day follow-up period, apart from a significant short-term decrease in fibronectin. No differences were observed in the plasma proteomes of donors with high versus low Hb and/or ferritin levels. Plasma proteins with the highest variation between and within donors included pregnancy zone protein, which was associated with sex, Alfa 1-antitrypsin which was associated with the allelic variation, and Immunoglobulin D. Coexpression analysis revealed clustering of proteins that are associated with platelet, red cell, and neutrophil signatures as well as with the complement system and immune responses, including a prominent correlating cluster of immunoglobulin M (IgM), immunoglobulin J chain (JCHAIN), and CD5 antigen-like (CD5L). DISCUSSION Overall, our proteomic approach shows that whole blood donation has a limited impact on the plasma proteins measured. Our findings suggest that plasma profiling can be successfully employed to consistently detect proteins and protein complexes that reflect the functionality and integrity of platelets, red blood cells, and immune cells in blood donors and thus highlights its potential use for donor health monitoring.
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Affiliation(s)
- Iris C Kreft
- Laboratory of Proteomics, Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Arie J Hoogendijk
- Laboratory of Proteomics, Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Carmen van der Zwaan
- Laboratory of Proteomics, Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Floris P J van Alphen
- Laboratory of Proteomics, Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Mariette Boon-Spijker
- Laboratory of Proteomics, Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Femmeke Prinsze
- Donor Studies, Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
| | - Alexander B Meijer
- Laboratory of Proteomics, Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands
| | - Dirk de Korte
- Department of Blood Cell Research, Sanquin Research, Amsterdam, The Netherlands
- Department of Product and Process Development, Sanquin Blood Bank, Amsterdam, The Netherlands
| | - Katja van den Hurk
- Donor Studies, Department of Donor Medicine Research, Sanquin Research, Amsterdam, The Netherlands
| | - Maartje van den Biggelaar
- Laboratory of Proteomics, Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
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Woessmann J, Kotol D, Hober A, Uhlén M, Edfors F. Addressing the Protease Bias in Quantitative Proteomics. J Proteome Res 2022; 21:2526-2534. [PMID: 36044728 PMCID: PMC9552229 DOI: 10.1021/acs.jproteome.2c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Protein quantification strategies using multiple proteases
have
been shown to deliver poor interprotease accuracy in label-free mass
spectrometry experiments. By utilizing six different proteases with
different cleavage sites, this study explores the protease bias and
its effect on accuracy and precision by using recombinant protein
standards. We established 557 SRM assays, using a recombinant protein
standard resource, toward 10 proteins in human plasma and determined
their concentration with multiple proteases. The quantified peptides
of these plasma proteins spanned 3 orders of magnitude (0.02–70
μM). In total, 60 peptides were used for absolute quantification
and the majority of the peptides showed high robustness. The retained
reproducibility was achieved by quantifying plasma proteins using
spiked stable isotope standard recombinant proteins in a targeted
proteomics workflow.
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Affiliation(s)
- Jakob Woessmann
- Science for Life Laboratory, KTH─Royal Institute of Technology, SE-171 65 Solna, Sweden.,Department of Protein Science, KTH─Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - David Kotol
- Science for Life Laboratory, KTH─Royal Institute of Technology, SE-171 65 Solna, Sweden.,Department of Protein Science, KTH─Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Andreas Hober
- Science for Life Laboratory, KTH─Royal Institute of Technology, SE-171 65 Solna, Sweden.,Department of Protein Science, KTH─Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH─Royal Institute of Technology, SE-171 65 Solna, Sweden.,Department of Protein Science, KTH─Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH─Royal Institute of Technology, SE-171 65 Solna, Sweden.,Department of Protein Science, KTH─Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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Kotol D, Hober A, Strandberg L, Svensson AS, Uhlén M, Edfors F. Targeted proteomics analysis of plasma proteins using recombinant protein standards for addition only workflows. Biotechniques 2021; 71:473-483. [PMID: 34431357 DOI: 10.2144/btn-2021-0047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Targeted proteomics is an attractive approach for the analysis of blood proteins. Here, we describe a novel analytical platform based on isotope-labeled recombinant protein standards stored in a chaotropic agent and subsequently dried down to allow storage at ambient temperature. This enables a straightforward protocol suitable for robotic workstations. Plasma samples to be analyzed are simply added to the dried pellet followed by enzymatic treatment and mass spectrometry analysis. Here, we show that this approach can be used to precisely (coefficient of variation <10%) determine the absolute concentrations in human plasma of hundred clinically relevant protein targets, spanning four orders of magnitude, using simultaneous analysis of 292 peptides. The use of this next-generation analytical platform for high-throughput clinical proteome profiling is discussed.
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Affiliation(s)
- David Kotol
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Linnéa Strandberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anne-Sophie Svensson
- Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
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Lill JR, Mathews WR, Rose CM, Schirle M. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics 2021; 18:503-526. [PMID: 34320887 DOI: 10.1080/14789450.2021.1962300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. AREAS COVERED Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. EXPERT OPINION Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.
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Affiliation(s)
- Jennie R Lill
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - William R Mathews
- OMNI Department, Genentech Inc. 1 DNA Way, South San Francisco, CA, USA
| | - Christopher M Rose
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - Markus Schirle
- Chemical Biology and Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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