PXD039343 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | A gas phase fractionaction scheme integrating ion mobility for rapid diaPASEF library generation |
Description | Data independent acquisition (DIA or DIA/SWATH ) mass spectrometry has emerged as a primary measurement strategy in the field of quantitative proteomics. diaPASEF is a recent adaptation that leverages trapped ion mobility spectrometry (TIMS) to improve selectivity and increase sensitivity. The complex fragmentation spectra generated by co-isolation of peptides in DIA mode are most typically analyzed with reference to prior knowledge in the form of spectral libraries. The best established method for generating libraries uses data dependent acquisition (DDA) mode, or DIA mode if appropriately deconvoluted, often including offline fractionation to increase depth of coverage,to create spectral libraries. More recently strategies for spectral library generation based on gas phase fractionation (GPF), where a representative sample is injected serially using narrow window DIA methods designed to cover different slices of the precursor space, have been introduced and performed comparably to deep offline fractionation-based libraries for DIA data analysis. Here, we investigated whether an analogous GPF-based library building approach that accounts for the ion mobility (IM) dimension is useful for the analysis of diaPASEF data and can remove the need for offline fractionation. To enable a rapid library development approach for diaPASEF we designed a GPF acquisition scheme covering the majority of multiply charged precursors in the m/z vs 1/K0 space requiring 7 injections of a representative sample and compared this with libraries generated by direct deconvolution-based analysis of diaPASEF data or by deep offline fractionation and ddaPASEF. . We found that the GPF based library outperformed library generation by direct deconvolution of the diaPASEF data, and performed comparably to deep offline fractionation libraries, when analysing diaPASEF data acquired from 200ng of commercial HeLa digest. With the ion mobility integrated GPF scheme we establish a pragmatic approach to rapid and comprehensive library generation for the analysis of diaPASEF data. |
HostingRepository | PRIDE |
AnnounceDate | 2023-08-18 |
AnnouncementXML | Submission_2023-08-18_09:15:54.942.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | JackPenny |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | acetylated residue; iodoacetamide derivatized residue |
Instrument | Bruker Daltonics timsTOF series |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-01-09 07:54:19 | ID requested | |
⏵ 1 | 2023-08-18 09:15:55 | announced | |
2 | 2023-11-14 07:05:28 | announced | 2023-11-14: Updated project metadata. |
Publication List
Keyword List
submitter keyword: diaPASEF,DIA, Spectral Library |
Contact List
BenCollins |
contact affiliation | Queen's University Belfast |
contact email | ben.collins@qub.ac.uk |
lab head | |
JackPenny |
contact affiliation | Queen's University Belfast |
contact email | jpenny02@qub.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD039343
- Label: PRIDE project
- Name: A gas phase fractionaction scheme integrating ion mobility for rapid diaPASEF library generation