PXD007528-1

PXD007528 is an original dataset announced via ProteomeXchange.

Title	Global ion suppression limits the potential of mass spectrometry based phosphoproteomics
Description	Mass spectrometry-based proteomics has become the method of choice to pinpoint and monitor thousands of post-translational modifications, predominately phosphorylation sites, in cellular signaling studies. Critical for achieving this analytical depth is the enrichment for phosphorylated peptides prior to LC-MS analysis. Despite the high prevalence of this modification, the numbers of identified phosphopeptides are lower than those achieved for unmodified peptides, and the cause for this still remains controversial. Here we introduce an effective phosphatase protocol that considerably improves global ionization efficiency and therefore overall sensitivity and coverage of standard phosphoproteomics studies. We demonstrate the power of our method on the model system of Salmonella-infected macrophages by extending the current quantitative picture of immune signaling pathways involved in infection.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_10:09:06.294.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD007528
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	Phospho; Oxidation; Carbamidomethyl
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-22 03:43:11	ID requested
⏵ 1	2024-10-07 10:09:07	announced

Dreier RF, Ahrn, é E, Broz P, Schmidt A, Global Ion Suppression Limits the Potential of Mass Spectrometry Based Phosphoproteomics. J Proteome Res, 18(1):493-507(2019) [pubmed]

10.1021/acs.jproteome.8b00812;

10.6019/PXD007528;

curator keyword: Technical

submitter keyword: macrophages,TMT, phosphoproteomics, infection, ion supression, LC-MS/MS

Alexander Schmidt
contact affiliation	Biozentrum, University of Basel, Klinglebergstrasse 50/70, CH-4056 Basel
contact email	alex.schmidt@unibas.ch
lab head
Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007528
     1. Label: PRIDE project
     2. Name: Global ion suppression limits the potential of mass spectrometry based phosphoproteomics