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PXD011225

PXD011225 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMaxQuant.Live enables global targeting of more than 25,000 peptides
DescriptionMass spectrometry (MS)-based proteomics is generally performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. While achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be measured in each run. In contrast, targeted proteomics aims to reproducibly and sensitively fragment a restricted number of precursors in each run, based on pre-scheduled mass-to-charge and retention time windows. Here we set out to merge these two concepts by a global targeting approach in which an arbitrary number of previously measured precursors is detected in real-time, followed by standard fragmentation or advanced peptide-specific analyses. We made use of a fast application programming interface to a quadrupole Orbitrap instrument and recalibration in mass, retention time and intensity dimensions to predict peptide identity. MaxQuant.Live is freely available and has a graphical user interface to specify many pre-defined data acquisition strategies. Controlling the acquisition with MaxQuant.Live rather than the vendor software, we observed no decline in acquisition speed. The power of our approach is demonstrated with the acquisition of breakdown curves for thousands of precursors of interest. It is also possible to uncover precursors that are not even visible in MS1 scans, using elution time prediction based on co-eluting isotope standards or the auto-adjusted, predicted retention time alone. Finally, we demonstrate that more than 25,000 precursors can be successfully recognized and targeted in single LC-MS runs. We conclude that global targeting combines the advantages of two classical approaches in MS-based proteomics, while expanding the analytical toolbox with many new possibilities.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:49:07.140.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMario Oroshi
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-09-28 07:50:10ID requested
12019-02-27 03:30:38announced
22019-06-03 01:34:37announcedUpdated publication reference for PubMed record(s): 30755466.
32024-10-22 04:49:08announced2024-10-22: Updated project metadata.
Publication List
Wichmann C, Meier F, Virreira Winter S, Brunner AD, Cox J, Mann M, MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides. Mol Cell Proteomics, 18(5):982-994(2019) [pubmed]
10.1074/mcp.TIR118.001131;
Keyword List
curator keyword: Technical
submitter keyword: proteomics,mass spectrometry
Contact List
Matthias Mann
contact affiliationDepartment of Proteomics and Signal Transduction Max Planck Institute of Biochemistry
contact emailmmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliationProteomics
contact emailoroshi@biochem.mpg.de
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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