SearchGUI

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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. […]

[…] 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 […]

[…] 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 […]