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ProteomicsImproved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline
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...
ORGANISM(S): Bos taurus (Bovine) Saccharomyces cerevisiae (Baker's yeast) 
2023-01-18 | PXD037492 | Pride
Kojak Crosslinking mass spectrometry Proteomics Software tools Protein interaction Peptideprophet Xl-ms Trans-proteomic pipeline Computational proteomics Iprophet 
UnknownKOJAK encodes a cellulose synthase-like protein required for root hair cell morphogenesis in Arabidopsis.
Not available
S-EPMC312599 | biostudies-literature
UnknownKojak: efficient analysis of chemically cross-linked protein complexes.
Not available
S-EPMC4428575 | biostudies-literature
ProteomicsABRF iPRG 2023 crosslinking study - Kojak COMPLETE results
The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year (2023) the iPRG group has put together a crosslinking study. The goal is to teach people how to analyze crosslinked samples...
ORGANISM(S): Escherichia coli 
2024-10-17 | PXD056910 | Pride
Iprg2023 Benchmark Crosslinking 
UnknownImproved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.
Not available
S-EPMC10234491 | biostudies-literature
ProteomicsXilmass: a new approach towards the identification of cross-linked peptides
Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient interactions. Moreover, cross-linking complements several structure determination approaches such as cryo-EM. Although several computational approaches are...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080758 | MassIVE
ProteomicsReanalysis of Cross-Linking Mass Spectrometry data from a ribisomal cellular fraction for benchmarking purposes
Reanalysis of a cross-linked ribosomal cellular fraction dataset, that is a subset of a fragmentation parameters optimization dataset (PRIDE project PXD006131). The HCD fragmented part of the dataset was searched with the Cross-Linking MS identification tools OpenPepXL, pLink2, Kojak and XiSearch.
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD014520 | Pride
Technical dataset Cross-linking Bs3 
ProteomicsXilmass: a new approach towards the identification of cross-linked peptides
Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient interactions. Moreover, cross-linking complements several structure determination approaches such as cryo-EM. Although several computational approaches are...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003880 | Pride
Calmodulin Cross-linking The actin-binding domain (abd) of plectin Dss Human 
ProteomicsCross-linking mass spectrometry analysis of trimeric complex of CRM1, SNP1 and RanGTP cross-linked with BS3
An X-ray crystallography structure of the trimeric nuclear export complex of CRM1, SNP1 and RanGTP is available on the PDB database with the ID 3GJX. To get an XL-MS dataset of a clean sample of a stable protein complex for benchmarking purposes, another sample from the protein expression, purificat...
ORGANISM(S): Escherichia coli 
2020-10-20 | PXD014359 | Pride
Technical dataset 
UnknownECL: an exhaustive search tool for the identification of cross-linked peptides using whole database.
Not available
S-EPMC4874008 | biostudies-literature
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