A Compendium of Murine (Phospho)Peptides Encompassing Different Isobaric Labeling and Data Acquisition Strategies

Targeted mass spectrometry-based
assays typically rely on previously
acquired large data sets 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 data sets 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 data sets 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. The data sets were of similar depth, and while overlap
across data sets was modest, protein overlap was high, thus reinforcing
the comprehensiveness of these data sets. The data also supported
FAIMS as a means to increase data set depth. These data sets provide
a rich resource of peptides that may be used as starting points for
targeted assays. Future data sets may be compiled for any genome-sequenced
organism using the technologies and strategies highlighted herein.
The data have been deposited in the ProteomeXchange Consortium with
data set identifier PXD024298.