FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Ignacy Rzagalinski - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Aliona Bogdanova - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Bharath Kumar Raghuraman - , University Cancer Centre Dresden, Medical Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Eric R Geertsma - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Lena Hersemann - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Tjalf Ziemssen - , Department of Neurology, Center of Clinical Neuroscience, University Vascular Centre, Department of Child and Adolescent Psychiatry and Psychotherapy (Author)
  • Andrej Shevchenko - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)

Abstract

Absolute (molar) quantification of clinically relevant proteins determines their reference values in liquid and solid biopsies. The FastCAT (for Fast-track QconCAT) method employs multiple short (<50 kDa), stable-isotope labeled chimeric proteins (CPs) composed of concatenated quantotypic (Q)-peptides representing the quantified proteins. Each CP also comprises scrambled sequences of reference (R)-peptides that relate its abundance to a single protein standard (bovine serum albumin, BSA). FastCAT not only alleviates the need to purify CP or use sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but also improves the accuracy, precision, and dynamic range of the absolute quantification by grouping Q-peptides according to the expected abundance of the target proteins. We benchmarked FastCAT against the reference method of MS Western and tested it in the direct molar quantification of neurological markers in human cerebrospinal fluid at the low ng/mL level.

Details

Original languageEnglish
Pages (from-to)1408-1417
Number of pages10
JournalJournal of proteome research
Volume21
Issue number6
Publication statusPublished - 3 Jun 2022
Peer-reviewedYes

External IDs

PubMedCentral PMC9171895
Scopus 85131177251
ORCID /0000-0001-8799-8202/work/171553560

Keywords

Keywords

  • Electrophoresis, Polyacrylamide Gel, Humans, Peptides/metabolism, Proteins, Proteomics/methods, Reference Standards

Library keywords