S. cerevisiae DDA orbitrap-based benchmark datasets. C4PR_LIV

ABSTRACT: In this study, label free peptide intensities from a well quantitatively characterised yeast cell lysate were acquired on two orbitrap mass spectrometers (LTQ-Velos and Q Exactive HF). Additionally, samples containing Universal Proteomics Standard and the Proteomics Dynamic range Standard (http://www.sigmaaldrich.com/life-science/proteomics/mass-spectrometry/ups1-and-ups2-proteomic.html) in a yeast background were also acquired. The absolute abundances of over 340 proteins present in that yeast lysate (determined in a parallel SRM-based study) were then used in order to determine the flyability (or detectability) of thousands of peptides. The flyability scores, termed the ‘F-factors’, reflect how well a peptide ionises in a complex chromatographically separated sample. Specifically, F-factors are calculated by normalising peptide precursor ion intensity by the absolute abundance of its parent protein. Based on the analysis of the six datasets deposited here (reflecting different gradients and instrument platforms) the study found that physicochemical properties including peptide length, charge and hydrophobicity are predictors of peptide detectability. Furthermore, it was established that hydrophobicity has a non-linear relationship with detectability and that coelution with competing ions significantly affects peptide detectability. The analysis based on the data deposited here suggests that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex chromatographically-separated peptide mixtures. The concept of F-factors will also undoubtedly assist in better surrogate selection in targeted mass spectrometry studies and allow more accurate calibration of peptide ion signal in label-free workflows.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Andrew Jarnuczak  

LAB HEAD: Professor Simon Hubbard

PROVIDER: PXD003472 | Pride | 2017-08-09

REPOSITORIES: Pride