PXD008211

PXD008211 is an original dataset announced via ProteomeXchange.

Title	Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements
Description	Increasing 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:41:29.042.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-14 09:15:04	ID requested
1	2018-06-05 08:51:58	announced
⏵ 2	2024-10-22 04:41:29	announced	2024-10-22: Updated project metadata.

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]

curator keyword: Technical

submitter keyword: LC-MSMS, Phosphoproteomics, TiO2, PRM,E.coli, QExactive, DDA

Boris Macek
contact affiliation	Prof. Dr. Boris Macek Quantitative Proteomics Proteome Center Tuebingen Interfaculty Institute for Cell Biology University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen Germany
contact email	boris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliation	University of Rouen
contact email	nalpas.nicolas@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008211
     1. Label: PRIDE project
     2. Name: Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements