PXD018189 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | capsPASEF – Collisional Cross Section Assisted Precursor Selection Applied to Cross-linking Mass Spectrometry |
Description | Ion mobility separates molecules in the gas-phase on their physico-chemical properties, providing information about their size as collisional cross-sections. The timsTOF Pro combines trapped ion mobility with a quadrupole, HCD cell and a time-of-flight mass spectrometer, to interrogate ions at high speeds with on-the-fly fragmentation. Ion mobility is perfectly suited for cross-linking mass spectrometry, which aims to uncover spatial restraints for proteins. The used cross-linking reagents covalently link amino acids in close proximity, resulting in peptide pairs after proteolytic digestion. This technique however suffers in terms of the low abundance of cross-linked peptides, which is partially resolved with enrichable cross-linking reagents. This class of reagents enables selective enrichment of cross-linking reagent modified peptides, resulting in selection of the cross-linked peptide pairs and peptides connected to a partially hydrolyzed reagent – termed mono-links. Even though mono-links carry limited structural information, for experiments aiming to uncover protein interactions in an unbiased manner they are unwanted byproducts. Gas-phase separation by IM has the potential to separate the two products and, indeed, we find separation between mono-links and cross-linked peptide pairs for PhoX cross-linked proteins. Moreover, an easy-to-interpret division at a CCS of 500 Å and a mono-isotopic mass of 2 kDa is present, which can be used for precursor selection. From our experiments on low complexity protein systems, sequencing of 50 - 70% of the mono-links is prevented, allowing the mass spectrometer the focus on sequencing the relevant cross-links. Application to a highly complex lysate focusing provides a 10-50 % increase in detected cross-links. |
HostingRepository | PRIDE |
AnnounceDate | 2023-05-15 |
AnnouncementXML | Submission_2023-05-15_02:04:18.573.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | RichardScheltema |
SpeciesList | scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Fusion |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-03-25 03:34:30 | ID requested | |
1 | 2020-07-24 01:24:58 | announced | |
⏵ 2 | 2023-05-15 02:04:19 | announced | 2023-05-15: Updated project metadata. |
Publication List
Steigenberger B, van den Toorn HWP, Bijl E, Greisch JF, R, ä, ther O, Lubeck M, Pieters RJ, Heck AJR, Scheltema RA, Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry. Mol Cell Proteomics, 19(10):1677-1687(2020) [pubmed] |
Keyword List
ProteomeXchange project tag: EPIC-XS |
submitter keyword: Ion Mobility,Cross-linking mass spectrometry, XL-MS, PhoX |
Contact List
Richard AlexanderScheltema |
contact affiliation | 1. Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. 2. Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands. |
contact email | r.a.scheltema@uu.nl |
lab head | |
RichardScheltema |
contact affiliation | Utrecht University |
contact email | r.a.scheltema@uu.nl |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD018189
- Label: PRIDE project
- Name: capsPASEF – Collisional Cross Section Assisted Precursor Selection Applied to Cross-linking Mass Spectrometry