This page last modified: Mar 07 2006
title:How to run SPC ISB tools. keywords:seattle,proteome,center,spc,proteomics,tools,nhlbi,proteomics,center,institute,systems,biology description:How to run readw.exe, msxml2other.exe, dtafilter, sequest27.exe, out2summary, interact. You must install cygwin and the SPC applications. However, the instructions for running these are very misleading, and the scripts that run other scripts have serious errors. Below are comments and the commands that worked. Apparently this sequence of commands was intended to be run by a shell script under cygwin. However, the shell script doesn't work, and the commands themselves are fairly easy to run (at least for a single run). If you do this many times, you'll need to get a programmer to write you a shell script, or even a Perl script (ActiveState makes a very nice free Perl for Windows). You might consider these to be examples. (The authors of these scripts at SPC/ISB should feel free to contact me to shed light on why the original scripts failed. The failures mostly had to do with incorrect path assumptions and missing or incorrectly named files within the scripts. The cygwin shell error messages made it fairly easy for a Linux/Unix programmer (me) to guess the original author's intentions and run the proper commands.) #Create a .mzXML file from the .RAW file: readw.exe 3stds.RAW c # Try this command (my recollection is that the command # is msxml2other.exe not msxml2other (without the .exe): msxml2other.exe -dta 3stds.mzXML # If msxml2other.exe does not create a folder 3stds, then create that # folder manually and rerun msxml2other.exe mkdir 3stds # Copy the sequest.params file into the 3stds folder: cp sequest.params 3stds/ # Change directory into the 3stds folder: cd 3stds # Filter (delete) dta files not meeting certain criteria: dtafilter -A -P15 # Search all dta files. Here is a find command that should work: find . -name "*.dta" -print | xargs /cygdrive/c/Xcalibur/system/programs/Bioworks.browser/sequest27.exe # Create a summary 3stds.html file in the directory above 3stds: out2summary . > ../3stds.html # Change directory to the folder above 3stds: cd ../ # Run Interact.