PXD029792 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Improved identification of proteoforms using FAIMS with internal CV stepping in top-down proteomics |
Description | In 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. |
HostingRepository | PRIDE |
AnnounceDate | 2022-02-28 |
AnnouncementXML | Submission_2022-02-28_03:11:05.876.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Andreas Tholey |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-11-17 23:48:24 | ID requested | |
⏵ 1 | 2022-02-28 03:11:06 | announced | |
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 affiliation | Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany |
contact email | a.tholey@iem.uni-kiel.de |
lab head | |
Andreas Tholey |
contact affiliation | Systematic Proteome Research & Bioanalytics, University of Kiel |
contact email | a.tholey@iem.uni-kiel.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD029792
- Label: PRIDE project
- Name: Improved identification of proteoforms using FAIMS with internal CV stepping in top-down proteomics