PXD024298

PXD024298 is an original dataset announced via ProteomeXchange.

Title	A compendium of murine (phospho)peptides encompassing different isobaric labeling and data acquisition strategies
Description	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.
HostingRepository	PRIDE
AnnounceDate	2021-06-03
AnnouncementXML	Submission_2021-06-03_08:43:09.369.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-22 02:10:42	ID requested
⏵ 1	2021-06-03 08:43:10	announced

Popow O, Liu X, Haigis KM, Gygi SP, Paulo JA, A Compendium of Murine (Phospho)Peptides Encompassing Different Isobaric Labeling and Data Acquisition Strategies. J Proteome Res, 20(7):3678-3688(2021) [pubmed]

submitter keyword: targeted proteomics, 3T3, FAIMS, eclipse, TMT, TMTpro

Joao A. Paulo
contact affiliation	Cell Biology Harvard Medical School USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/06/PXD024298

PRIDE project URI

• PRIDE
  1. PXD024298
     1. Label: PRIDE project
     2. Name: A compendium of murine (phospho)peptides encompassing different isobaric labeling and data acquisition strategies