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PXD029792

PXD029792 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleImproved identification of proteoforms using FAIMS with internal CV stepping in top-down proteomics
DescriptionIn top-down (TD) proteomics, fractionation prior to mass spectrometric (MS) analysis is a crucial step for the high confidence identification of proteoforms and increased sample depth. In addition to liquid phase separations, gas-phase fractionation strategies such as field asymmetric ion mobility spectrometry (FAIMS) have been shown to be highly beneficial in TD proteomics. However, the need for multiple injections using different compensation voltages (CV) leads to a huge increase in measurement time and the amount of sample required. Therefore, we here investigated for the first time the use of internal CV stepping for single shot TD analysis, i.e., the application of multiple CVs per acquisition. In addition, MS parameters were optimized for the individual CVs since different CVs target certain mass ranges. For example, small proteoforms identified mainly with lower CVs can be identified with a lower resolution and number of microscans than larger proteins identified mainly with higher CVs. We investigated the optimal combination and number of CVs for different gradient lengths and validated the optimized settings with the low molecular weight proteome of CaCo 2 cells obtained by different sample preparation techniques. Compared to measurements without FAIMS, both the number of identified protein groups (+60-94%) and proteoforms (+46-127%), and their confidence were significantly increased, while the measurement time remained identical. In total, we identified 684 protein groups and 2,675 proteoforms from CaCo-2 cells in less than 24 hours using the optimized multi-CV method.
HostingRepositoryPRIDE
AnnounceDate2022-02-28
AnnouncementXMLSubmission_2022-02-28_03:11:05.876.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAndreas Tholey
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-11-17 23:48:24ID requested
12022-02-28 03:11:06announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: top-down, proteomics, FAIMS, human cell line, CaCo-2
Contact List
Andreas Tholey
contact affiliationSystematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
contact emaila.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliationSystematic Proteome Research & Bioanalytics, University of Kiel
contact emaila.tholey@iem.uni-kiel.de
dataset submitter
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Dataset FTP location
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