Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

  • Author: Edfors, Fredrik

    KTH - Royal Institute of Technology, Sweden

  • Author: Forsström, Björn

    KTH - Royal Institute of Technology, Sweden

  • Author: Vunk, Helian

    KTH - Royal Institute of Technology, Sweden

  • Author: Kotol, David

    KTH - Royal Institute of Technology, Sweden

  • Author: Fredolini, Claudia

    KTH - Royal Institute of Technology, Sweden

  • Author: Maddalo, Gianluca

    KTH - Royal Institute of Technology, Sweden

  • Author: Svensson, Anne Sophie

    KTH - Royal Institute of Technology, Sweden

  • Author: Boström, Tove

    KTH - Royal Institute of Technology, Sweden

  • Author: Tegel, Hanna

    KTH - Royal Institute of Technology, Sweden

  • Author: Nilsson, Peter M.

    KTH - Royal Institute of Technology, Sweden

  • Author: Schwenk, Jochen M.

    KTH - Royal Institute of Technology, Sweden

  • Author: Uhlén, Mathias

    High Throughput Molecular Bioscience, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark

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The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.
Original languageEnglish
JournalJournal of Proteome Research
Volume18
Issue number7
Pages (from-to)2706-2718
ISSN1535-3893
DOIs
Publication statusPublished - 2019
CitationsWeb of Science® Times Cited: No match on DOI

ID: 186197255