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Protocols

SearchGUI specifications

Information


Unique identifier OMICS_03352
Name SearchGUI
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl
License Apache License version 2.0
Computer skills Advanced
Version 3.3.3
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Marc Vaudel

Additional information


https://github.com/compomics/searchgui/wiki

Publications for SearchGUI

SearchGUI citations

 (41)
library_books

Identification of a unique Radical SAM methyltransferase required for the sp3 C methylation of an arginine residue of methyl coenzyme M reductase

2018
Sci Rep
PMCID: 5943407
PMID: 29743535
DOI: 10.1038/s41598-018-25716-x

[…] The raw mass spectrometric data were converted to mgf-files using MSConvert. SearchGUI software (v3.2.17) and the OMSSA search engine were used for peptide identification. The data were searched against the M. acetivorans proteome database obtained from UniProt (Taxon identifi […]

call_split

Hookworm Secreted Extracellular Vesicles Interact With Host Cells and Prevent Inducible Colitis in Mice

2018
Front Immunol
PMCID: 5936971
PMID: 29760697
DOI: 10.3389/fimmu.2018.00850
call_split See protocol

[…] ry of adventitious proteins (cRAP) appended to it. Database search was performed using Mascot Versions 2.4 (Matrix Science Ltd., London, UK) and X!Tandem, MS-GF+, OMSSA, and Tide search engines using SearchGUI (). The same parameters were used as described in Ref. ().The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository with th […]

call_split

Intrinsically disordered N termini in human parechovirus 1 capsid proteins bind encapsidated RNA

2018
Sci Rep
PMCID: 5895611
PMID: 29643409
DOI: 10.1038/s41598-018-23552-7
call_split See protocol

[…] g an Accela HPLC. Peptide RCAP data was generated on a Bruker Autoflex III MALDI-ToF and analyzed using GPMAW (General Protein/Mass Analysis for Windows, Supplementary Figure ).Database searches used searchGUI and the peptide sequences were compiled with peptideshaker,. Databases were created using HPeV1 protein sequences appended to a FASTA file containing the uniprot human proteome and the commo […]

library_books

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics

2018
BMC Res Notes
PMCID: 5856202
PMID: 29544540
DOI: 10.1186/s13104-018-3289-6

[…] nd to integrate with RAId useful visualization and graphic tools, we have developed the first GUI for RAId. Although there exist other freely available proteomics analysis GUI such as OMSSAGUI [] and SearchGUI [], RAId_GUI is the only one that provides not only peptide/protein identifications with accurate statistics but also a large collection of additional functionalities. […]

library_books

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy P Framework

2018
Proteomes
PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] tch, OMSSA, Comet, Myrimatch, MS-Amanda and Novor), X!Tandem was determined to have a balance of speed and sensitivity that made it a good choice, especially for a training resource. The outputs from SearchGUI are further filtered and statistically analyzed using the companion PeptideShaker tool [], which provides outputs compatible with downstream processing. provides detailed instructions on th […]

library_books

Homeolog expression analysis in an allotriploid non model crop via integration of transcriptomics and proteomics

2018
Sci Rep
PMCID: 5777989
PMID: 29358676
DOI: 10.1038/s41598-018-19684-5

[…] om Progenesis and were identified against its proper database integrating 3 database search algorithms: Mascot, v 2.2.06, X!Tandem, version X!Tandem Vengeance (2015.12.15.2), and MS-GF+, v 10282. The SearchGUI identification settings were as follows: enzyme trypsin, 2 missed cleavages (maximally), 10.0 ppm as MS1 and 0.02 Da as MS2 tolerance, Carbamidomethylation of C (+57.021464 Da) as fixed modi […]

Citations

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SearchGUI institution(s)
Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
SearchGUI funding source(s)
Supported by the Research Council of Norway and the Bergen Research Foundation.

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