Sentence examples for mouse protein database from inspiring English sources
SILAC-labeled proteins were identified and quantified with MaxQuant version 1.5.2.8 software89 with the Uniprot mouse protein database containing 89,422 proteins, to which 175 commonly observed contaminants and all the reversed sequences had been added.
Peptides from ICAT samples were identified by searching MS/MS spectra against the same mouse protein database using Sequest [24].
Searches in the mouse protein database resulted in 6 possible peptides containing 8 cysteine residues within a mass tolerance window of ±50 ppm from Hep-1 (Table S1).
PMF analysis was done with a MASCOT server version 2.1 (Matrix Science, London, U.K). taking the UniProtKB mouse protein database (taxonomy: mus musculus).
The acquired MS/MS spectra were searched with SEQUEST algorithm against a composite target-decoy mouse protein database consisting of the protein sequences (target) downloaded from SWISSPROT mouse protein database (downloaded July 2006) and reversed versions of these sequences (decoy) as described [28].
Mass spectra collected by MALDI-QqTOF and MALDI-ion trap mass spectrometers were analyzed by the computer search engines ProFound (http://prowl.rockefeller.edu/prowl-cgi/profound.exe), Xproteo (http://www.xproteo.com) and GPM (http://prowl.rockefeller.edu/tandem/thegpm_tandem.html) using the NCBI non-redundant mouse protein database.
Spectra were collected for analysis and searched through mouse protein databases using Mascot and imported into Scaffold® (Proteomesoftware).
Three-dimensional coordinates for available crystal structures of START domains, either unbound (mouse STARD4 (Protein Database (PDB) 1JSS) and mouse MLN64 (PDB 1EM2)) or ligand-bound (human PCTP (PDB 1LN1)) were obtained from Brookhaven Protein Structure Database.
We then removed redundant sequences and predicted ncRNAs with sequences similar or identical to coding genes annotated in the Mouse RefSeq mRNA database [ 19], RIKEN cDNA [ 7], Mouse Protein NR database [ 20], or coding genes in other organisms annotated in GenBank [ 21].
MS/MS spectra were searched by the Sequest algorithm against a database containing the mouse DGAT1 protein database and its reversed complement.
Tandem mass spectra were searched against mouse IPI protein database using SEQUEST algorism with a 3Da peptide mass tolerance [19].
