PXD037492 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2023-01-18 |
AnnouncementXML | Submission_2023-01-18_08:32:57.598.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | MichaelHoopmann |
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: Kojak,crosslinking mass spectrometry, proteomics, software tools, protein interaction, PeptideProphet, XL-MS, Trans-Proteomic Pipeline, computational proteomics, iProphet |
Contact List
Robert L.Moritz |
contact affiliation | Institute for Systems Biology, USA |
contact email | rmoritz@systemsbiology.org |
lab head | |
MichaelHoopmann |
contact affiliation | Institute for Systems Biology |
contact email | michael.hoopmann@systemsbiology.org |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD037492
- Label: PRIDE project
- Name: Improved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline