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Protocols

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 citations

 (19)
library_books

Structural and Immunodiagnostic Characterization of Synthetic Antigen B Subunits From Echinococcus granulosus and Their Evaluation as Target Antigens for Cyst Viability Assessment

2017
PMCID: 5905600
PMID: 29149256
DOI: 10.1093/cid/cix1006

[…] ng 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) []. […]

call_split

Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins

2017
PLoS One
PMCID: 5658093
PMID: 29073188
DOI: 10.1371/journal.pone.0186840
call_split See protocol

[…] 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 […]

library_books

CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

2017
Nat Commun
PMCID: 5648754
PMID: 29051543
DOI: 10.1038/s41467-017-01241-9

[…] ak 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 toleranc […]

call_split

Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe–S cluster assembly centers† †Electronic supplementary information (ESI) available: Fig. S1–S14; Tables S1 and S2. See DOI: 10.1039/c7mt00089h

2017
PMCID: 5552075
PMID: 28548666
DOI: 10.1039/c7mt00089h
call_split See protocol

[…] The program StavroX 3.5.1 (www.stavrox.com/help.php) calculated all theoretical combinations of cross-linked peptides between Yfh1 and Isu1 and within Yfh1 or Isu1 and compared them to each of the two MS/MS datas […]

library_books

The chaperonin CCT inhibits assembly of α synuclein amyloid fibrils by a specific, conformation dependent interaction

2017
Sci Rep
PMCID: 5244355
PMID: 28102321
DOI: 10.1038/srep40859

[…] t raw MS/MS data to an mgf file that was searched against a custom-made database containing the sequences of human α-syn and of different bovine CCT subunits. The MS/MS ion search was performed using StavroX 3.5.1 with the following settings: trypsin as enzyme allowing 2 and 3 missed cleavages for Arg and Lys residues, respectively, oxidation of Met as variable modification, DSP/DTSSP as crosslink […]

library_books

Cellular localization of relaxin‐like gonad‐stimulating peptide expression in Asterias rubens: New insights into neurohormonal control of spawning in starfish

2016
PMCID: 5396301
PMID: 27806429
DOI: 10.1002/cne.24141

[…] nd could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. Proteins sharing significant peptide evidence were grouped into clusters. The program Stavrox (v. 3.6.0) was used to search for crosslinked spectra (Gotze et al., ). Default settings were used except that semitryptic digestion was permitted, disulfide bonds were specified as the crossl […]


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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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