PXD011225

PXD011225 is an original dataset announced via ProteomeXchange.

Title	MaxQuant.Live enables global targeting of more than 25,000 peptides
Description	Mass 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:49:07.140.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-28 07:50:10	ID requested
1	2019-02-27 03:30:38	announced
2	2019-06-03 01:34:37	announced	Updated publication reference for PubMed record(s): 30755466.
⏵ 3	2024-10-22 04:49:08	announced	2024-10-22: Updated project metadata.

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;

curator keyword: Technical

submitter keyword: proteomics,mass spectrometry

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
dataset submitter

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/2019/02/PXD011225

PRIDE project URI

• PRIDE
  1. PXD011225
     1. Label: PRIDE project
     2. Name: MaxQuant.Live enables global targeting of more than 25,000 peptides