PXD037492

PXD037492 is an original dataset announced via ProteomeXchange.

Title	Improved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline
Description	Fragmentation ion spectral analysis of chemically crosslinked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify crosslinked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable crosslinkers, and identification of crosslinks between 15N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of crosslinks improve the sensitivity and accuracy of correct crosslink identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multi-platform.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:02:31.119.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michael Hoopmann
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-17 01:31:23	ID requested
1	2023-01-18 08:32:58	announced
⏵ 2	2023-11-14 08:02:31	announced	2023-11-14: Updated project metadata.

Hoopmann MR, Shteynberg DD, Zelter A, Riffle M, Lyon AS, Agard DA, Luan Q, Nolen BJ, MacCoss MJ, Davis TN, Moritz RL, Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline. J Proteome Res, 22(2):647-655(2023) [pubmed]

submitter keyword: Kojak,crosslinking mass spectrometry, proteomics, software tools, protein interaction, PeptideProphet, XL-MS, Trans-Proteomic Pipeline, computational proteomics, iProphet

Robert L. Moritz
contact affiliation	Institute for Systems Biology, USA
contact email	rmoritz@systemsbiology.org
lab head
Michael Hoopmann
contact affiliation	Institute for Systems Biology
contact email	michael.hoopmann@systemsbiology.org
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/2023/01/PXD037492

PRIDE project URI

• PRIDE
  1. PXD037492
     1. Label: PRIDE project
     2. Name: Improved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline