PXD016554-1

PXD016554 is an original dataset announced via ProteomeXchange.

Title	An experimentally generated peptide database increases the sensitivity in XL-MS of complex samples
Description	The application of non-cleavable cross-linkers to complex samples in XL-MS workflows is limited by the n² problem, a quadratic expansion of the search space with increasing database size. Here, a peptide-focused approach is proposed, for which cross-linking peptide candidates are identified in a parallel experiment by using a thiol-cleavable cross-linker with equal reactivity. Samples are reduced and alkylated, thereby releasing cross-linked peptides with a variable modification on the initially cross-linked residue. Modified peptides are identified by database search and concatenated to a peptide database, which is finally used for the analysis of the sample cross-linked with a non-cleavable cross-linker. This way, the search space is dramatically reduced leading to a higher sensitivity, because there is less chance for random hits to false positive sequences. The approach was benchmarked on cross-linked purified protein complexes (20 S Proteasome, yeast PolII, and TFIIH), and in vivo cross-linked bacteria (Bacillus subtilis, Bacillus cereus) by comparing it to the conventional approach of searching against the protein sequences.
HostingRepository	PRIDE
AnnounceDate	2020-03-26
AnnouncementXML	Submission_2020-03-26_03:30:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Iwan Parfentev
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-03 05:10:03	ID requested
⏵ 1	2020-03-26 03:30:40	announced

Parfentev I, Schilbach S, Cramer P, Urlaub H, An experimentally generated peptide database increases the sensitivity of XL-MS with complex samples. J Proteomics, 220():103754(2020) [pubmed]

curator keyword: Technical, Biological

submitter keyword: XL-MS, Cross-linking, Peptide database, 20 S proteasome, TFIIH, PolII, Bacillus subtilis, Bacillus cereus

Henning Urlaub
contact affiliation	Bioanalytical Mass Spectrometry group, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
contact email	henning.urlaub@mpibpc.mpg.de
lab head
Iwan Parfentev
contact affiliation	Max-Planck-Institute for Biophysical Chemistry
contact email	iwan.parfentev@mpibpc.mpg.de
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/2020/03/PXD016554

PRIDE project URI

• PRIDE
  1. PXD016554
     1. Label: PRIDE project
     2. Name: An experimentally generated peptide database increases the sensitivity in XL-MS of complex samples