PXD010895 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Non-covalently associated peptides are observed during liquid chromatography-mass spectrometry and affect cross-link analyses |
Description | Cross-Linking/mass spectrometry draws structural information out of covalently linked peptide pairs. When these links do not match to previous structural models they may indicate changes of protein conformation. Unfortunately, such links can also be the result of experimental errors or artefacts. Here we describe the observation of non-covalently associated peptides during liquid chromatography-mass spectrometry analysis which can easily be misidentified as cross-linked. Strikingly, they often mismatch to the protein structure or may falsely suggest protein homo-dimerization. Non-covalently associated peptides presumably form during ionization and can be distinguished from cross-linked peptides by observing co-elution of the corresponding linear peptides in MS1, as well as the presence of the individual peptide fragments in mixed MS2 spectra. Interestingly, non-covalently associated peptides seem sensitive to ionization source design as we see them more prevalently on a Q Exactive than on an Orbitrap Velos mass spectrometer. Finally we show how more disruptive ionization settings such as moderate in-source fragmentation suppresses their presence. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_04:12:50.645.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Sven Giese |
SpeciesList | scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF; LTQ Orbitrap Velos; Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-08-28 04:02:41 | ID requested | |
1 | 2019-01-25 00:36:47 | announced | |
⏵ 2 | 2024-10-22 04:12:51 | announced | 2024-10-22: Updated project metadata. |
Publication List
10.1021/acs.analchem.8b04037; |
Giese SH, Belsom A, Sinn L, Fischer L, Rappsilber J, Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses. Anal Chem, 91(4):2678-2685(2019) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: cross-linking, HSA, SDA |
Contact List
Juri Rappsilber |
contact affiliation | 1. Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany 2. Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH93BF, United Kingdom ( lab head ) |
contact email | juri.rappsilber@tu-berlin.de |
lab head | |
Sven Giese |
contact affiliation | Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany |
contact email | sven.giese@tu-berlin.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD010895
- Label: PRIDE project
- Name: Non-covalently associated peptides are observed during liquid chromatography-mass spectrometry and affect cross-link analyses