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Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry

Part of the Methods in Molecular Biology book series (MIMB,volume 1959)

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.

Key words

  • Mass spectrometry
  • Data-independent acquisition
  • Serum
  • Biomarker discovery
  • Label-free quantification

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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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Correspondence to Anne-Marie Hesse .

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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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