PXD058341

PXD058341 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Analysis of FAIMS for the Study of Affinity-Purified Protein Complexes Using the Orbitrap Ascend Tribrid Mass Spectrometer
Description	In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and an Orbitrap Ascend Tribrid Mass Spectrometer. Our primary objective was to evaluate the application of the FAIMS interface for detecting affinity purified SAP25 protein complexes with enhanced sensitivity and robustness. As a result, we observed that nanoLC-FAIMS-MS (with FAIMS) significantly improved the sensitivity and detection limits at the protein level, peptide level and significantly reduced chemical contaminants compared to nanoLC-MS alone without FAIMS (No FAIMS). This FAIMS configuration resulted in 42% and 92% increases for the total proteins and unique proteins, respectively, and 44% and 88% increases for total peptides and unique peptides compared to the No FAIMS configuration. Our in-depth comparison of FAIMS and No FAIMS shows that FAIMS outperforms by significantly reducing the missing value by <15% in datasets and plays a significant role in filtering chemical contaminants. Our findings highlight the potential of FAIMS with Orbitrap Ascend Tribrid Mass Spectrometer to enhance the depth of AP-MS analysis. The data were deposited with the MASSIVE repository with the identifiers.
HostingRepository	MassIVE
AnnounceDate	2024-12-03
AnnouncementXML	Submission_2024-12-03_12:19:55.511.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Michael Washburn
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Orbitrap Ascend

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-27 09:53:25	ID requested
⏵ 1	2024-12-03 12:19:55	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: FAIMS, AFFINITY PURIFICATION, QUANTITATIVE PROTEOMICS, DatasetType:Proteomics

submitter keyword: FAIMS, AFFINITY PURIFICATION, QUANTITATIVE PROTEOMICS, DatasetType:Proteomics

Contact List

Michael Washburn
contact affiliation	University of Kansas Medical Center
contact email	mwashburn4@kumc.edu
lab head
Michael Washburn
contact affiliation	KUMC
contact email	mwashburn4@kumc.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/MSV000096548/

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/MSV000096548/