PXD064164
PXD064164 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Jmod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics |
| Description | The throughput of mass spectrometry (MS) proteomics can be increased substantially by multiplexing that enables parallelization of data acquisition. Such parallelization in the mass domain (plexDIA) and the time domain (timePlex) increases the density of mass spectra and the overlap between ions originating from different precursors. To enhance sequence identification and quantification from such spectra, we developed an open source software for joint modeling: JMod. It uses the intrinsic structure in the spectra and explicitly models overlapping peaks as linear superpositions of their components. This modeling enabled performing 9-plexDIA using 2 Da offset PSMtags by deconvolving the resulting overlapping isotopic envelopes in both MS1 and MS2 space. The results demonstrate 9-fold higher throughput with preserved quantitative accuracy and coverage depth. This support for smaller mass offsets increases multiplexing capacity and thus proteomic throughput for a given plexDIA tag, and we demonstrate this generalizability with diethyl labeling. By supporting enhanced decoding of DIA spectra multiplexed in the mass and time domains, JMod provides an open and flexible software for increasing the throughput of sensitive proteomics. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-05-22 |
| AnnouncementXML | Submission_2025-05-22_10:22:06.285.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Kevin |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; common name: baker's yeast; NCBI TaxID: 4932; |
| ModificationList | Diethyl |
| Instrument | Orbitrap Astral; Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-05-21 12:25:24 | ID requested | |
| ⏵ 1 | 2025-05-22 10:22:06 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: DIA, plexDIA, PSMtag, DatasetType:Proteomics |
Contact List
| Nikola Slavov | |
|---|---|
| contact affiliation | Northeastern University |
| contact email | nslavov@northeastern.edu |
| lab head | |
| Kevin | |
| contact affiliation | PTI |
| contact email | kmcdonnell@parallelsq.org |
| 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-ftp.ucsd.edu/v09/MSV000097957/ |
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