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A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition

Vidova, Veronika, Spacil, Zdenek·2017·Analytica Chimica Acta
DOI 10.1016/j.aca.2017.01.059
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Abstract

Mass spectrometry (MS) based proteomics have achieved a near-complete proteome coverage in humans and in several other organisms, producing a wealth of information stored in databases and bioinformatics resources. Recent implementation of selected/multiple reaction monitoring (SRM/MRM) technology in targeted proteomics introduced the possibility of quantitatively follow-up specific protein targets in a hypothesis-driven experiment. In contrast to immunoaffinity-based workflows typically used in biological and clinical research for protein quantification, SRM/MRM is characterized by high selectivity, large capacity for multiplexing (approx. 200 proteins per analysis) and rapid, cost-effective transition from assay development to deployment. The concept of SRM/MRM utilizes triple quadrupole (QqQ) mass analyzer to provide inherent reproducibility, unparalleled sensitivity and selectivity to efficiently differentiate isoforms, post-translational modifications and mutated forms of proteins. SRM-like targeted acquisitions such as parallel reaction monitoring (PRM) are pioneered on high resolution/accurate mass (HR/AM) platforms based on the quadrupole-orbitrap (Q-orbitrap) mass spectrometer. The expansion of HR/AM also caused development in data independent acquisition (DIA). This review presents a step-by-step tutorial on development of SRM/MRM protein assay intended for researchers without prior experience in proteomics. We discus practical aspects of SRM-based quantitative prote…

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  • The limit of quantification typically reaches the low attomole range to several tens or even hundreds of attomoles, depending on peptide ionization properties and sample matrix complexity.

    “The limit of quantification typically reaches the low attomole range (1 attomole = (10−18 mol) × (6.022 × 1023 molecules/mol) = 6.022 × 105 molecules) to several tens or even hundreds of attomoles, depending on peptide ionization properties and sample matrix complexity (35, 36).”

    From Lipidome and proteome of astrocyte and microglia ApoE lipoprotein reveal differences based on cell type and ApoE isoform (2026) · cites this paper as [36]

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Metadata

Authors
Vidova, V., & Spacil, Z.
ORCID
Spacil, Zdenek
Venue
Analytica Chimica Acta
Publisher
Elsevier BV
Published
2017-04
Volume
964
Pages
7-23
ISSN
0003-2670
DOI
10.1016/j.aca.2017.01.059
Cited by
352
References
12
Language
en
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Funders
  • RECETOX research infrastructure (LM2015051)
  • CETOCOEN PLUS (CZ.02.1.01/0.0/0.0/15_003/0000469)

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