PXD020704

PXD020704 is an original dataset announced via ProteomeXchange.

Title	Open search strategy for inferring the masses of cross-link adducts
Description	Development of new reagents for protein cross-linking is continually ongoing. The chemical formulas of the linker adducts formed by these reagents are usually deduced from expert knowledge, and then validated by mass spectrometry. Clearly, it would have been more rigorous if the adduct masses are inferred directly from the data without any prior assumption on the chemistries. Unfortunately, the analysis tools that are currently available to detect chemical modifications on linear peptides are not applicable to the case of two cross-linked peptides. Here we show that an adaptation of the open search strategy that works on linear peptides can be used to study cross-link modifications between pairs of peptides. We benchmark our approach by correctly inferring the linker masses of two well-known reagents - DSS and formaldehyde - to accuracies of a few parts per million. We then investigate the cross-linking chemistries of two poorly characterized reagents - EMCS and glutaraldehyde. In the case of EMCS, we find that the expected cross-linking chemistry is accompanied by a competing chemistry that targets other amino acid types. In the case of glutaraldehyde, we find that the chemical formula of the dominant linker is C5H4, which indicates a ringed aromatic structure. These results demonstrate that, at very little effort, our approach can yield non-trivial insights to facilitate the studies of new cross-linkers.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_04:21:37.332.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Moriya Slavin
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-03 02:40:37	ID requested
⏵ 1	2021-09-09 04:21:38	announced

Slavin M, Tayri-Wilk T, Milhem H, Kalisman N, Open Search Strategy for Inferring the Masses of Cross-Link Adducts on Proteins. Anal Chem, 92(24):15899-15907(2020) [pubmed]

submitter keyword: Mass spectrometry, Modifications, open search, Cross-linking, XL-MS, EMCS, Glutaraldehyde

Nir Kalisman
contact affiliation	Dept. of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel (lab head)
contact email	nirka@mail.huji.ac.il
lab head
Moriya Slavin
contact affiliation	Biochemistry department in the Hebrew University
contact email	moriya.slavin@mail.huji.ac.il
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD020704

PRIDE project URI

• PRIDE
  1. PXD020704
     1. Label: PRIDE project
     2. Name: Open search strategy for inferring the masses of cross-link adducts