Mass correct

From Mswiki

I wrote a program, mass_correct, for post-acquisition mass correction.

This program works on both MS1 and MS2 files. To use the program, navigate
to the folder that contains MS1 and/or MS2 files that need mass correction
due to systematic mass shift, and run the command:
 mass_correct -c ppm_offset

For example, if you know the systematic mass shift is -6.2 ppm, then run
this command:
 mass_correct -c -6.2

The program will create a folder "corrected" and put all the
mass-corrected MS1/MS2 files into that folder.

I tested the program on several data sets and it works fine -- actually,
after mass correction, you will get more protein IDs and peptide IDs.
Follow is an example. In this example, I get 10% more proteins and 20%
more peptides. In this example, the mass shift is -6 ppm. So I guess you
will get even more proteins/peptides if the mass shift is -10 ppm
something.

Before mass correction:

        Proteins        Peptide IDs     Spectra
Forward matches 891     1930    3058
Decoy matches   43      43      45
Forward FP rate 4.83    2.23    1.47

Mass shift information (before correction):
-6.15145317815541       1.3090068737608276      929     (non-modified pep)
-5.778947369650195      1.4903596918911706      1102 (modified pep)

After mass correction:

        Proteins        Peptide IDs     Spectra
Forward matches 1004    2332    3709
Decoy matches   48      48      48
Forward FP rate 4.78    2.06    1.29

Mass shift information (after correction):
-0.1645161300611787     0.9261886797676555      1147     (non-modified
pep)
0.13488873033881274     0.9128045115395435      1393   (modified pep)

Contact: bingwlu (at) scripps dot edu to send your feedback.