PXD010895

PXD010895 is an original dataset announced via ProteomeXchange.

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

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.

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]

curator keyword: Technical

submitter keyword: cross-linking, HSA, SDA

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

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PRIDE project URI

• PRIDE
  1. PXD010895
     1. Label: PRIDE project
     2. Name: Non-covalently associated peptides are observed during liquid chromatography-mass spectrometry and affect cross-link analyses