Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective.

Our data set compares: (i) SRM on a AB Sciex Qtrap 5500 (ii) SRM on a Thermo Scientific TSQ Vantage (iii) PRM on a Thermo Scientific Q Exactive (iv) DIA on an AB Sciex TripleTOF 5600 and (v) DIA on a Thermo Scientific Q Exactive HF. A pre-digested protein sample with a priori known analyte quantities (mixture of six trypsin-digested human proteins and 14 corresponding synthetic, heavy, stable isotope labeled (SIL) peptides) was targeted in a complex yeast matrix on all platforms. In the first part of the study, the quantitative accuracy and precision was investigated at constant analyte quantities (8 technical replicates). In the second part of the study, the impact of decreasing analyte quantities on analytical performance was studied over a concentration range of three orders of magnitude (3 technical replicates per dilution step). A full description of the data set is available at http://onlinelibrary.wiley.com/doi/10.1002/pmic.201500502/abstract
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http://fgcz-intranet.uzh.ch/tiki-index.php?page=MSQC1
http://bioconductor.org/packages/msqc1/
https://panoramaweb.org/labkey/MSQC1.url

Keywords: 

  • proteomics
  • label-free
  • LC-MS
  • PRM
  • SRM
  • DIA