Colander
From Mswiki
Colander is a MS/MS data pre-processing program for selecting CID MS/MS
spectra generated from phosphopeptides.
To run Colander, follow the following steps.
1. ssh to Grunt (ssh grunt.scripps.edu);
2. cd to the directory where your MS2 files are located.
3. Type the command "colander.pl &" (The & sign is to instruct the program to be run in the background. The Perl program will call
a Java program to carry out the spectra selection task);
More example commands:
colander.pl 0.5: This is the default, where Colander uses 0.5 as the
probability cutoff.
colander.pl 0.9: This instructs Colander to use 0.9 as the probability
cutoff. Only spectra that are highly likely to be generated from phosphopeptides
will pass the filter.
colander.pl 0.2: This is a loose probability cutoff.
colander.pl -1: Nothing will be filtered out. However, every
spectrum will be assigned a probability score.
4. The program might take a few hours to run;
5. The Colander program will create a folder "colander". MS/MS spectra that are
One scenario of using Colander:
You have don't the regular database search on the MS/MS data. And now you want
to check whether there are phosphorylated peptides for this MS/MS data. The
solution is to filter the MS/MS data with Colander and then do the
phosphorylation database search.
Colander was developed by Bingwen Lu and Cristian Ruse. Please report bug and send feedback to bingwlu (at) scripps.edu or cruse (at) scripps.edu.
To Cite Colander, Use This Reference
* Bingwen Lu, Cristian Ruse, John Yates III (2008) Colander: A probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search. Journal of Proteome Research, In Press.
