SearchGUI

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] (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 […]