PXD008211 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
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/2018/06/PXD008211 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD008211
- Label: PRIDE project
- Name: Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements