PXD032821

PXD032821 is an original dataset announced via ProteomeXchange.

Title	Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers
Description	Proteome-wide crosslinking mass spectrometry studies have coincided with the advent of MS-cleavable crosslinkers that can reveal the individual masses of the two crosslinked peptides. However, recently such studies have also been published with non-cleavable crosslinkers suggesting that MS-cleavability is not essential. We therefore examined in detail the advantages and disadvantages of using the commonly used MS-cleavable crosslinker, DSSO. Indeed, DSSO gave rise to signature peptide fragments with a distinct mass difference (doublet) for nearly all identified crosslinked peptides. Surprisingly, we could show that it was not these peptide masses that proved the main advantage of MS-cleavability of the crosslinker, but improved peptide backbone fragmentation which reduces ambiguity of peptide identifications. This also holds true for another commonly used MS-cleavable crosslinker, DSBU. We show, furthermore, that the more intricate MS3-based data acquisition approaches lack sensitivity and specificity, causing them to be outperformed by the simpler and faster stepped HCD method. This understanding will guide future developments and applications of proteome-wide crosslinking mass spectrometry.
HostingRepository	PRIDE
AnnounceDate	2022-06-24
AnnouncementXML	Submission_2022-06-24_00:23:15.143.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lars Kolbowski
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	monomethylated residue; monohydroxylated residue; deamidated residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos; Orbitrap Fusion; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-26 14:15:52	ID requested
⏵ 1	2022-06-24 00:23:15	announced

Kolbowski L, Lenz S, Fischer L, Sinn LR, O'Reilly FJ, Rappsilber J, Improved Peptide Backbone Fragmentation Is the Primary Advantage of MS-Cleavable Crosslinkers. Anal Chem, 94(22):7779-7786(2022) [pubmed]

submitter keyword: Crosslinking, CLMS, LC-MSMS, MS-cleavable crosslinker, DSSO, DSBU

Juri Rappsilber
contact affiliation	Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany
contact email	juri.rappsilber@tu-berlin.de
lab head
Lars Kolbowski
contact affiliation	TU Berlin
contact email	lars.kolbowski@tu-berlin.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD032821
     1. Label: PRIDE project
     2. Name: Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers