PXD016662 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients |
Description | State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 minute LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins. |
HostingRepository | PRIDE |
AnnounceDate | 2020-02-18 |
AnnouncementXML | Submission_2020-02-17_17:18:40.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Dorte Bekker-Jensen |
SpeciesList | scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-12-09 05:30:49 | ID requested | |
⏵ 1 | 2020-02-17 17:18:42 | announced | |
2 | 2020-11-06 08:43:12 | announced | 2020-11-06: Updated project metadata. |
Publication List
Bekker-Jensen DB, Mart, í, nez-Val A, Steigerwald S, R, ü, ther P, Fort KL, Arrey TN, Harder A, Makarov A, Olsen JV, A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. Mol Cell Proteomics, 19(4):716-729(2020) [pubmed] |
Keyword List
submitter keyword: Bottom-up Shotgun proteomics, Orbitrap, DIA, FAIMS, DDA, phosphoproteomics, TMT |
Contact List
Jesper Velgaard Olsen |
contact affiliation | Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark |
contact email | jesper.olsen@cpr.ku.dk |
lab head | |
Dorte Bekker-Jensen |
contact affiliation | University of Copenhagen |
contact email | dorte.bekker-jensen@cpr.ku.dk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD016662
- Label: PRIDE project
- Name: A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients