A compendium of murine (phospho)peptides encompassing different isobaric labeling and data acquisition strategies

ABSTRACT: Targeted mass spectrometry-based assays typically rely on previously acquired large datasets for peptide target selection. Such repositories are widely available for unlabeled peptides. However, they are less common for isobaric tagged peptides. Here we have assembled two series of six datasets originating from a mouse embryonic fibroblast cell line (NIH/3T3). One series is of peptides derived from a tryptic digest of a whole cell proteome and a second from enriched phosphopeptides. These datasets encompass three labeling approaches (unlabeled, TMT11-labeled and TMTpro16-labeled) and two data acquisition strategies (ion trap MS2 with and without FAIMS-based gas phase separation). We identified a total of 1,509,526 peptide-spectrum matches which covered 11,482 proteins from the whole cell proteome tryptic digest, and 188,849 phosphopeptides from the phosphopeptide enrichment. For each series, the datasets were of similar depth, but peptide overlap across datasets was modest. We then examined differences in characteristics and physicochemical properties of dataset-unique peptide sequences. These datasets provide a rich resource of peptides which may be used as starting points for targeted assays. Future datasets may be compiled for any genome-sequenced organism using the technologies and strategies highlighted herein.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Joao Paulo  

LAB HEAD: Joao A. Paulo

PROVIDER: PXD024298 | Pride | 2021-06-03

REPOSITORIES: Pride