StavroX specifications

Information


Unique identifier OMICS_12419
Name StavroX
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A sequences cleavage sites modifications / cross-linker, cross-linkable residues / precursor MS/MS spectra
Input format mgf
Output data A table of all peptides of proteins / table of all fragment ions with labeled identified ions / MS/MS spectrum with labeled ions / result table with scores of all cross-link candidates
Operating system Windows
Programming languages Java
Computer skills Medium
Version 3.6.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andrea Sinz <>

Publication for StavroX

StavroX in publications

 (16)
PMCID: 5905600
PMID: 29149256
DOI: 10.1093/cid/cix1006

[…] liquid chromatography–tandem ms performed with a q exactive mass spectrometer [] interfaced with an ultimate 3000 rslcnano liquid chromatography system. cross-linked peptides were identified using stavrox software (version 3.3.0.1) []., western immunoblotting was performed as described elsewhere []. membranes were incubated with 1:200 working standard anti-echinococcus serum, human (wsh […]

PMCID: 5658093
PMID: 29073188
DOI: 10.1371/journal.pone.0186840

[…] ms/ms analysis alone were grouped to satisfy the principles of parsimony. proteins sharing peptides with significant sequence homologies were grouped into clusters., to identify crosslinked peptides stavrox version 3.5.1 [] and plink version 1.23 [] were used for ms/ms data interpretation with the following settings. cleavage enzyme and specificity: trypsin (specific cleavage); protease cleavage […]

PMCID: 5648754
PMID: 29051543
DOI: 10.1038/s41467-017-01241-9

[…] lists using in-house script (pava, ucsf). generated peak lists were searched against eighteen proteins making up the u1snrnp from s. cerevisiae of the swiss-prot database (update 2017_01_24) using stavrox (v3.6.0.1). search parameters included carbamidomethylation-c as a fixed modification, oxidation-m and bs3 as variable modifications, allowing for two missed cleavages. precursor mass […]

PMCID: 5244355
PMID: 28102321
DOI: 10.1038/srep40859

[…] serines must be at approximately this distance to be crosslinked. we were thus able to obtain information about neighbouring regions surrounding the contact site., the results were analysed using stavrox software, which identified four intermolecular crosslinks involving cct and α-syn a53t at a false discovery rate (fdr) < 0.05 (, ). all cct residues were located inside the cct cavity. […]

PMCID: 5108309
PMID: 27512953
DOI: 10.1038/cddis.2016.200

[…] molecular weights, many migrated to different positions () indicating extensive protein processing., the mass spectrometry data obtained from identified proteins were examined with the software, stavrox for the possible presence of bis-ɛ-lysyl polyamine and ɛ-lysyl-s-methionyl polyamine cross-links, which can be generated by chlorinated polyamines as well as bis-γ-glutamyl polyamine […]


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StavroX institution(s)
Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany; Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
StavroX funding source(s)
Supported by the DFG (German Research Foundation, projects Si 867/13-1 and Si 867/15-1) and the BMBF (ProNet-T3, Project To-06), by the Graduiertenkolleg 1591 Posttranscriptional Control of Gene Expression: Mechanisms and Role in Pathogenesis”, by the Graduiertenkolleg 1026 “Conformational Transitions in Macromolecular Interactions” at the Martin-Luther University Halle-Wittenberg and by the EU (LUNGTARGET project).

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