tools

Documentation

Overview

A set of tools using the unthermo library

The labelq tool inserts iTRAQ reporter ions from HCD scans in CID spectra.

Program output is MGF formatted MS2 spectra

The peakstats tool outputs a few data about the peaks of supplied ions:

• Mass, Time at Maximum, Maximal intensity of ions found in the LC/MS map
• Full width at half maximum of this maximal peak

The printspectrum tool prints out the spectrum (mz and intensity values) of a Thermo RAW File

Every line of the output is a peak registered by the mass spectrometer
characterized by an m/z value in Da and an intensity in the mass spectrometer's unit of abundance

The XIC tool prints mass chromatograms for a specific m/z.

For the m/z given, it prints the peak with highest intensity in interval
[mz-tol ppm,mz+tol ppm] for every MS-1 scan.

Every line contains the retention time and intensity of a found peak

Example:
    xic -mz 361.1466 -tol 2.5 -raw rawfile.raw

Output:
    0.003496666666666667 10500.583
    0.015028333333333333 11793.04
    0.03391333333333333 10178.598
    0.05393333333333334 10671.821
    0.07350833333333334 11572.251