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PXD016554 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAn experimentally generated peptide database increases the sensitivity in XL-MS of complex samples
DescriptionThe 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterIwan Parfentev
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListacetylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-12-03 05:10:03ID requested
12020-03-26 03:30:40announced
Publication List
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]
Keyword List
curator keyword: Technical, Biological
submitter keyword: XL-MS, Cross-linking, Peptide database, 20 S proteasome, TFIIH, PolII, Bacillus subtilis, Bacillus cereus
Contact List
Henning Urlaub
contact affiliationBioanalytical Mass Spectrometry group, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
contact emailhenning.urlaub@mpibpc.mpg.de
lab head
Iwan Parfentev
contact affiliationMax-Planck-Institute for Biophysical Chemistry
contact emailiwan.parfentev@mpibpc.mpg.de
dataset submitter
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