PXD052383
PXD052383 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | diaTracer enables spectrum-centric analysis of diaPASEF proteomics data |
| Description | Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (m/z, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved "pseudo-MS/MS" spectra, facilitating direct ("spectral-library free") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from cerebrospinal fluid (CSF) and plasma samples, data from phosphoproteomics and HLA immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass offset searches. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-12-02 |
| AnnouncementXML | Submission_2024-12-02_09:40:19.492.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Fengchao |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Oxidation; Phospho; Acetyl; Glu->pyro-Glu; Gln->pyro-Glu; Cysteinyl; Carbamidomethyl |
| Instrument | timsTOF Pro; timsTOF HT; timsTOF Ultra |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-05-19 13:11:50 | ID requested | |
| ⏵ 1 | 2024-12-02 09:40:19 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: timsTOF, diaPASEF, data-independent acquisition, peptide identification, spectrum centric |
Contact List
| Alexey I. Nesvizhskii | |
|---|---|
| contact affiliation | University of Michigan, Ann Arbor, MI, US |
| contact email | nesvi@umich.edu |
| lab head | |
| Fengchao | |
| contact affiliation | University of Michigan |
| contact email | yufe@umich.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/v07/MSV000094803/ |
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