GPMAW

GPMAW WWW.gpmaw.com Protein sequence and mass analysis Commerdal... 

GPMAW software by Lighthouse Data (beta-version 8.01 a5, Odense, Denmark)... 

The multisequence FASTA file was uploaded to the GPMAW software (version 8.01a5) and processed to produce individual text files containing in silico fragment ions for each protein sequence. The header line of each text file shows the ExPASy accession nunaber, the protein name. 

The files were sorted by file size, and the largest files were opened and examined to confirm that the calculated protein MW was within the MW search tolerance but also taking into account that proteins with cysteine residues are retrieved from ExPASy in their reduced form (-SH) but are calculated by GPMAW in the oxidized form (-S-S-). Files of larger than normal size may indicate retrieval of protein sequences having attached signal peptides, which, when removed, produce a posttranslationally modified protein MW, which falls within the search MW. The... 

ExPASy accession numbers of these signal peptide-containing protein sequences were noted and separately retrieved from ExPASy. The signal peptides were removed from the sequence. The length of a signal peptide was indicated by ExPASy. These modified protein sequences were then combined into a single file, uploaded, and processed by GPMAW. 

Batch process PASTA file GPMAW Output text files containing in silico fragment ions of each sequence... 

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