KTH Uhlen Lab - PrEST resource

Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics

  • Organism: Homo sapiens
  • Instrument: Q Exactive HF
  • SpikeIn: Yes
  • Keywords: SIL, Recombiant protein fragment, Plasma
  • Lab head: Fredrik Edfors
Abstract
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-labelled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labelled recombinant proteins prior to 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.
Created on 5/31/19, 11:32 AM
Clustergrammer Heatmap
Flag FileDownloadCreatedProteinsPeptidesPrecursorsTransitionsReplicates
all combined_2019-03-21_20-40-14.sky.zip (46 MB)2019-05-31133575268,5337
20180518 multiplex quantification - APOA4 only samples_2018-05-18_12-13-20.sky.zip (265 MB)2019-05-311364864
20180518 multiplex quantification only samples_2018-05-18_11-58-07.sky.zip (380 MB)2019-05-3128357050268
20180509_prest-kinetics_2018-05-09_18-52-06.sky.zip (120 MB)2019-05-311613628684820