Abstract
In discovery proteomics experiments, tandem mass spectrometry and data-dependent acquisition (DDA) are classically used to identify and quantify peptides and proteins through database searching. This strategy suffers from known limitations such as under-sampling and lack of reproducibility of precursor ion selection in complex proteomics samples, leading to somewhat inconsistent analytical results across large datasets. Data-independent acquisition (DIA) based on fragmentation of all the precursors detected in predetermined isolation windows can potentially overcome this limitation. DIA promises reproducible peptide and protein quantification with deeper proteome coverage and fewer missing values than DDA strategies. This approach is particularly attractive in the field of clinical biomarker discovery, where large numbers of samples must be analyzed. Here, we describe a DIA workflow for non-depleted serum analysis including a straightforward approach through which to construct a dedicated spectral library, and indications on how to optimize chromatographic and mass spectrometry analytical methods to produce high-quality DIA data and results.
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References
Parker CE, Borchers CH (2014) Mass spectrometry based biomarker discovery, verification, and validation—Quality assurance and control of protein biomarker assays. Mol Oncol 8:840–858. https://doi.org/10.1016/j.molonc.2014.03.006
Liu H, Wang H, Hongmei Z et al (2018) Preliminary study of protein changes in trisomy 21 fetus by proteomics analysis in amniocyte. Prenat Diagn 38(6):435–444. https://doi.org/10.1002/pd.5259
Rauniyar N, Yu X, Cantley J et al (2018) Quantification of urinary protein biomarkers of autosomal dominant polycystic kidney disease by parallel reaction monitoring. Proteomics Clin Appl 12(5):e1700157. https://doi.org/10.1002/prca.201700157
Preece RL, Han SYS, Bahn S (2018) Proteomic approaches to identify blood-based biomarkers for depression and bipolar disorders. Expert Rev Proteomics 15(4):325–340. https://doi.org/10.1080/14789450.2018.1444483
Atak A, Khurana S, Gollapalli K et al (2018) Quantitative mass spectrometry analysis reveals a panel of nine proteins as diagnostic markers for colon adenocarcinomas. Oncotarget 9:13530–13544. https://doi.org/10.18632/oncotarget.24418
Geyer PE, Kulak NA, Pichler G et al (2016) Plasma proteome profiling to assess human health and disease. Cell Syst 2:185–195. https://doi.org/10.1016/j.cels.2016.02.015
Sandow JJ, Rainczuk A, Infusini G et al (2018) Discovery and validation of novel protein biomarkers in ovarian cancer patient urine. Proteomics Clin Appl 12(3):e1700135. https://doi.org/10.1002/prca.201700135
Hirao Y, Saito S, Fujinaka H et al (2018) Proteome profiling of diabetic mellitus patient urine for discovery of biomarkers by comprehensive MS-based proteomics. Proteomes 6. https://doi.org/10.3390/proteomes6010009
Bostanci N, Selevsek N, Wolski W et al (2018) Targeted proteomics guided by label-free global proteome analysis in saliva reveal transition signatures from health to periodontal disease. Mol Cell Proteomics 17(7):1392–1409. https://doi.org/10.1074/mcp.RA118.000718
Duriez E, Masselon CD, Mesmin C et al (2017) Large-scale SRM screen of urothelial bladder cancer candidate biomarkers in urine. J Proteome Res 16:1617–1631. https://doi.org/10.1021/acs.jproteome.6b00979
Anderson NL (2010) The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem 56:177–185. https://doi.org/10.1373/clinchem.2009.126706
Nahnsen S, Bielow C, Reinert K, Kohlbacher O (2013) Tools for label-free peptide quantification. Mol Cell Proteomics 12:549–556. https://doi.org/10.1074/mcp.R112.025163
Doll S, Dreßen M, Geyer PE et al (2017) Region and cell-type resolved quantitative proteomic map of the human heart. Nat Commun 8:1469. https://doi.org/10.1038/s41467-017-01747-2
Song E, Gao Y, Wu C et al (2017) Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. Sci Data 4:170091. https://doi.org/10.1038/sdata.2017.91
Gilquin B, Louwagie M, Jaquinod M et al (2017) Multiplex and accurate quantification of acute kidney injury biomarker candidates in urine using protein standard absolute quantification (PSAQ) and targeted proteomics. Talanta 164:77–84. https://doi.org/10.1016/j.talanta.2016.11.023
Venable JD, Dong M-Q, Wohlschlegel J et al (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 1:39–45. https://doi.org/10.1038/nmeth705
Navarro P, Kuharev J, Gillet LC et al (2016) A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol 34:1130–1136. https://doi.org/10.1038/nbt.3685
Röst HL, Rosenberger G, Navarro P, et al (2014) OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. In: Nat. Biotechnol. https://www.nature.com/articles/nbt.2841. Accessed 12 Apr 2018
Egertson JD, MacLean B, Johnson R et al (2015) Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat Protoc 10:887–903. https://doi.org/10.1038/nprot.2015.055
Tsou C-C, Avtonomov D, Larsen B et al (2015) DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258–264. https://doi.org/10.1038/nmeth.3255
Li Y, Zhong C-Q, Xu X et al (2015) Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files. Nat Methods 12:1105–1106. https://doi.org/10.1038/nmeth.3593
Bruderer R, Bernhardt OM, Gandhi T et al (2017) Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results. Mol Cell Proteomics 16:2296–2309. https://doi.org/10.1074/mcp.RA117.000314
Guo T, Kouvonen P, Koh CC et al (2015) Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med 21(4):407–413. https://doi.org/10.1038/nm.3807
Muntel J, Xuan Y, Berger ST et al (2015) Advancing urinary protein biomarker discovery by data-independent acquisition on a quadrupole-orbitrap mass spectrometer. J Proteome Res 14:4752–4762. https://doi.org/10.1021/acs.jproteome.5b00826
Song Y, Zhong L, Zhou J et al (2017) Data-independent acquisition-based quantitative proteomic analysis reveals potential biomarkers of kidney cancer. Proteomics Clin Appl 11. https://doi.org/10.1002/prca.201700066
Végvári Á, Welinder C, Lindberg H et al (2011) Biobank resources for future patient care: developments, principles and concepts. J Clin Bioinforma 1:24. https://doi.org/10.1186/2043-9113-1-24
Anderson NL, Anderson NG (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1:845–867
Keshishian H, Burgess MW, Gillette MA et al (2015) Multiplexed, quantitative workflow for sensitive biomarker discovery in plasma yields novel candidates for early myocardial injury. Mol Cell Proteomics 14:2375–2393. https://doi.org/10.1074/mcp.M114.046813
Bellei E, Bergamini S, Monari E et al (2011) High-abundance proteins depletion for serum proteomic analysis: concomitant removal of non-targeted proteins. Amino Acids 40:145–156. https://doi.org/10.1007/s00726-010-0628-x
Tu C, Rudnick PA, Martinez MY et al (2010) Depletion of abundant plasma proteins and limitations of plasma proteomics. J Proteome Res 9:4982–4991. https://doi.org/10.1021/pr100646w
Lin L, Zheng J, Yu Q et al (2018) High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis. J Proteomics 174:9–16. https://doi.org/10.1016/j.jprot.2017.12.014
Nigjeh EN, Chen R, Brand RE et al (2017) Quantitative proteomics based on optimized data-independent acquisition in plasma analysis. J Proteome Res 16:665–676. https://doi.org/10.1021/acs.jproteome.6b00727
Cox J, Hein MY, Luber CA et al (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 13:2513–2526. https://doi.org/10.1074/mcp.M113.031591
Bruderer R, Bernhardt OM, Gandhi T et al (2015) Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues. Mol Cell Proteomics 14(5):1400–1410. https://doi.org/10.1074/mcp.M114.044305
Trudgian DC, Fischer R, Guo X et al (2014) GOAT—a simple LC-MS/MS gradient optimization tool. Proteomics 14:1467–1471. https://doi.org/10.1002/pmic.201300524
Moruz L, Pichler P, Stranzl T et al (2013) Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics. Anal Chem 85:7777–7785. https://doi.org/10.1021/ac401145q
Zhang Y, Bilbao A, Bruderer T et al (2015) The use of variable Q1 isolation windows improves selectivity in LC-SWATH-MS acquisition. J Proteome Res 14:4359–4371. https://doi.org/10.1021/acs.jproteome.5b00543
Forshed J (2017) Experimental design in clinical 'Omics Biomarker Discovery. J Proteome Res 16:3954–3960. https://doi.org/10.1021/acs.jproteome.7b00418
Wiśniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359–362. https://doi.org/10.1038/nmeth.1322
Lebert D, Louwagie M, Goetze S et al (2015) DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. J Proteome Res 14:787–803. https://doi.org/10.1021/pr500834z
Gundry RL, White MY, Murray CI et al (2009) Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow. Curr Protoc Mol Biol Chapter 10:Unit10.25. https://doi.org/10.1002/0471142727.mb1025s88
Govaert E, Van Steendam K, Willems S et al (2017) Comparison of fractionation proteomics for local SWATH library building. Proteomics 17. https://doi.org/10.1002/pmic.201700052
Wieczorek S, Combes F, Lazar C et al (2017) DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. Bioinformatics 33:135–136. https://doi.org/10.1093/bioinformatics/btw580
Acknowledgment
This study was supported by grants from the “Investissement d’Avenir Infrastructures Nationales en Biologie et Santé” program (ProFI project, ANR-10-INBS-08) and by the French National Research Agency in the framework of the “Investissements d’avenir” program (GRAL project, ANR-10-LABX-49-01 and LIFE project, ANR-15-IDEX-02).
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Kraut, A. et al. (2019). Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry. In: Brun, V., Couté, Y. (eds) Proteomics for Biomarker Discovery. Methods in Molecular Biology, vol 1959. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9164-8_9
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DOI: https://doi.org/10.1007/978-1-4939-9164-8_9
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