PXD027242

PXD027242 is an original dataset announced via ProteomeXchange.

Title	Data-independent acquisition protease-multiplexing enables increased proteome sequence coverage across multiple fragmentation modes
Description	The 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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:52:31.710.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alicia Richards
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-12 01:48:14	ID requested
1	2022-03-10 17:09:17	announced
⏵ 2	2023-11-14 08:52:32	announced	2023-11-14: Updated project metadata.

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]

submitter keyword: DIA, GluC, multiplexing,AspN

Danielle L. Swaney
contact affiliation	University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
contact email	danielle.swaney@ucsf.edu
lab head
Alicia Richards
contact affiliation	Krogan lab
contact email	alicia.richards@ucsf.edu
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/2022/03/PXD027242

PRIDE project URI

• PRIDE
  1. PXD027242
     1. Label: PRIDE project
     2. Name: Data-independent acquisition protease-multiplexing enables increased proteome sequence coverage across multiple fragmentation modes