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PXD008211

PXD008211 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleParallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements
DescriptionIncreasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy more than two thirds of the proteome, the abundance of protein phosphorylation is much lower in bacteria. Even the state-of-the-art phosphopeptide enrichment protocols fail to remove the high background of abundant unmodified peptides, leading to low signal intensity and undersampling of phosphopeptide precursor ions in consecutive data-dependent MS runs. Consequently, large-scale bacterial phosphoproteomic datasets often suffer from poor reproducibility and a high number of missing values. Here we explore the application of parallel reaction monitoring (PRM) on a Q Exactive mass spectrometer in bacterial phosphoproteome analysis, focusing especially on run-to-run sampling reproducibility. In multiple measurements of identical phosphopeptide-enriched samples, we show that PRM outperforms DDA in terms of detection frequency, reaching almost complete sampling efficiency, compared to 20% in DDA. We observe a similar trend over multiple rounds of (heterogeneous) phosphopeptide-enriched samples and conclude that PRM is a method of choice in bacterial phosphoproteomics projects where reproducible detection and quantification of a relatively small set of phosphopeptides is desired.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:41:29.042.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterNicolas Nalpas
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListphosphorylated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-11-14 09:15:04ID requested
12018-06-05 08:51:58announced
22024-10-22 04:41:29announced2024-10-22: Updated project metadata.
Publication List
10.1016/j.jprot.2018.03.028;
Taumer C, Griesbaum L, Kovacevic A, Soufi B, Nalpas NC, Macek B, Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements. J Proteomics, 189():60-66(2018) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: LC-MSMS, Phosphoproteomics, TiO2, PRM,E.coli, QExactive, DDA
Contact List
Boris Macek
contact affiliationProf. Dr. Boris Macek Quantitative Proteomics Proteome Center Tuebingen Interfaculty Institute for Cell Biology University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen Germany
contact emailboris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliationUniversity of Rouen
contact emailnalpas.nicolas@gmail.com
dataset submitter
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