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PXD027242

PXD027242 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleData-independent acquisition protease-multiplexing enables increased proteome sequence coverage across multiple fragmentation modes
DescriptionThe use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments, but due to the additional sample preparation and analysis time required, it has not been widely adapted in routine proteomic workflows. While data-independent acquisition (DIA) has been primarily optimized for fragmenting tryptic peptides with beam type (bt)-CID, it has the potential to analyze multiplexed samples from different protease digests. Here we evaluate a DIA multiplexing method that combines three proteolytic digests (Trypsin, AspN, and GluC) into a single sample. We first optimize DIA conditions for both resonance excitation (re-CID) and bt-CID to determine the optimal consensus fragmentation conditions for tryptic and non-tryptic peptides, and apply these methods to a human cell line. We demonstrate that using this multiplexed approach results in similar protein identifications and quantitative performance as compared to trypsin alone, but enables up to a 63% increase in peptide detections, resulting in up to a 8% increase in average sequence coverage. Importantly, this resulted in 100% sequence coverage for numerous proteins, suggesting the utility of this approach in applications where sequence coverage is critical, such as proteoform analysis.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:52:31.710.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAlicia Richards
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListiodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-07-12 01:48:14ID requested
12022-03-10 17:09:17announced
22023-11-14 08:52:32announced2023-11-14: Updated project metadata.
Publication List
Richards AL, Chen KH, Wilburn DB, Stevenson E, Polacco BJ, Searle BC, Swaney DL, Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes. J Proteome Res, 21(4):1124-1136(2022) [pubmed]
Keyword List
submitter keyword: DIA, GluC, multiplexing,AspN
Contact List
Danielle L. Swaney
contact affiliationUniversity of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
contact emaildanielle.swaney@ucsf.edu
lab head
Alicia Richards
contact affiliationKrogan lab
contact emailalicia.richards@ucsf.edu
dataset submitter
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Dataset FTP location
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Repository Record List
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