How to change the SEQUEST browser data directory
Overview: This SEQUEST tip describes how to change the default directory where the SEQUEST browser looks for data files.
The SEQUEST browser is a great tool for doing SEQUEST searches. However, one of the limitations that exists is that you can't navigate directories where the SEQUEST browser looks for .RAW datafiles. This usually limits you to the Xcalibur data directory, most often C:\Xcalibur\data. If you're like everyone else using Windows NT, you have no disk space left on your C drive, so sticking more huge LC/MS runs there is another bad idea.
Ahh, but you can change the default SEQUEST directory, it's just not obvious where this is done. If you have not already noticed, the SEQUEST browser consists of a bunch of Perl scripts. What you need to do is edit a variable in one of the Perl scripts that hardcodes the data directory to a specific path. Here's what to do:
- Locate your Website Pro directory, or wherever you've installed the Website Pro server software. This is usually C:\Website. Look in the etc subdirectory (e.g., C:\Website\etc). There should be a file called microchem_var.pl. This is a Perl script which sets a bunch of initial variables for the SEQUEST browser. Use a notepad to open this TEXT (ASCII) file. (Note: I suggest making a backup of this file in case you muck something up by mistake and you can go back to the original). Look for the line which contains the $lcqdir variable. For example, it might look something like this:
$lcqdir = "C:\Xcalibur\data";
- Change the variable to match the desired path, for example, assuming you have a D:\data directory:
$lcqdir = "D:\data";
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Save the file. (Again make sure you backup the original with a different name first).
-
Try it out. Move some .RAW files to your new directory (in our case (D:\data). Go to your SEQUEST browser create dta files page (substitute the correct phrase for yourSequestBrowserSite in the URL below)
"http://yourSequestBrowserSite/cgi-bin/create_dta.pl"
- You should now see your data files in the Finnigan Data File dropdown box. Success! You've changed the default data directory for the SEQUEST browser!
- Read on, for more SEQUEST tips...
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