SearchGUI protocols

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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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Documentation


Maintainer


  • person_outline Marc Vaudel <>

Additional information


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

Publications for SearchGUI

SearchGUI in pipelines

 (2)
2018
PMCID: 5895611
PMID: 29643409
DOI: 10.1038/s41598-018-23552-7

[…] 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 […]

2017
PMCID: 5466729
PMID: 28615994
DOI: 10.1186/s12953-017-0119-z

[…] a concatenated target/decoy [] version of the ovis aries (27,284; 99.5%) complement of the uniprotkb, 27,411 (target) sequences. the decoy sequences were created by reversing the target sequences in searchgui. the identification settings were as follows: trypsin with a maximum of 1 missed cleavages; 10.0 ppm as ms1 and 0.5 da as ms2 tolerances; fixed modifications: carbamidomethylation of c […]


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SearchGUI in publications

 (37)
PMCID: 5943407
PMID: 29743535
DOI: 10.1038/s41598-018-25716-x

[…] acquired in the orbitrap at a resolution of 60,000 and a maximum injection time of 120 ms for orbitrap ms2 detection., 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 […]

PMCID: 5936971
PMID: 29760697
DOI: 10.3389/fimmu.2018.00850

[…] 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 […]

PMCID: 5856202
PMID: 29544540
DOI: 10.1186/s13104-018-3289-6

[…] 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., to run raid_gui […]

PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] the use of de novo spectral matching in tandem with traditional sequence database-dependent methods [], as well as the use of multiple database search algorithms, such as those offered by the searchgui tool [], to increase the numbers of confident metapeptide identifications. , for the workflow deployed in our informatics resource, we chose a relatively straightforward approach […]

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

[…] (crap, http://www.thegpm.org/crap/) and combined into a target/decoy database enabling false discovery rate (fdr) estimation. the decoy sequences were created by reversing the target sequences in searchgui v 3.1.4,., for every sample, peak lists (.mgf format) containing all msms spectra were extracted from progenesis and were identified against its proper database integrating 3 database […]


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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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