PXD011121

PXD011121 is an original dataset announced via ProteomeXchange.

Title	In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides
Description	Cross-linking/mass spectrometry has undergone a maturation process akin to standard proteomics by adapting key methods such as false discovery rate control and quantification. A seldom-used search setting in proteomics is the consideration of multiple (lighter) alternative values for the monoisotopic precursor mass to compensate for possible misassignments of the monoisotopic peak. Here, we show that monoisotopic peak assignment is a major weakness of current data handling approaches in cross-linking. Cross-linked peptides often have high precursor masses, which reduces the presence of the monoisotopic peak in the isotope envelope. Paired with generally low peak intensity, this generates a challenge that may not be completely solvable by precursor mass assignment routines. We therefore took an alternative route by ‘in-search assignment of the monoisotopic peak’ in the cross-linking search tool Xi (Xi-MPA), which considers multiple precursor masses during database search. We compare and evaluate the performance of established preprocessing workflows that partly correct the monoisotopic peak and Xi-MPA on three publicly available datasets. Xi-MPA always delivered the highest number of identifications with ~2 to 4-fold increase of PSMs without compromising identification accuracy as determined by FDR estimation and comparison to crystallographic models.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:15:22.879.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Swantje Lenz
SpeciesList	scientific name: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719); NCBI TaxID: 759272; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-18 02:12:55	ID requested
1	2019-04-05 04:09:07	announced
⏵ 2	2024-10-22 04:15:25	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.8b00600;

Lenz S, Giese SH, Fischer L, Rappsilber J, In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides. J Proteome Res, 17(11):3923-3931(2018) [pubmed]

curator keyword: Technical

submitter keyword: data processing,cross-linking mass spectrometry

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 EH9 3BF, United Kingdom
contact email	juri.rappsilber@tu-berlin.de
lab head
Swantje Lenz
contact affiliation	Technische Universität Berlin
contact email	swantje.lenz@tu-berlin.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/2019/04/PXD011121

PRIDE project URI

• PRIDE
  1. PXD011121
     1. Label: PRIDE project
     2. Name: In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides