precursors.py

###described in: Savitski et. al., Analytical Chemistry, 2011

To use the precursors.py script, first install mz e.g. by running pip install mz (a very useful distribution of Python which provides pip as well as many other useful tools for scientific scripting is Anaconda Python). Even if you have XCalibur installed on the machine, you should install the freely downloadable MSFileReader. You can install the script anywhere, however it is convenient to put a copy in the same directory as the files being characterized.

The script is run as follows:

python precursors.py rawfile [scanlist]

If a scanlist is specified, then only the precursors for the MS/MS scan numbers in the file will be characterized. The output is a tab-delimited text file made from the rawfile name with the suffix "_precursors.txt".

The script calculates the following quantities described in the manuscript, where each corresponds to one MS/MS spectrum:

SCAN - The scan number of the MS/MS whose precursor is being characterized.

TIME_min - Acquisition time (in minutes) of the MS/MS scan.

PRECURSOR - The precursor m/z.

CHARGE - The precursor charge.

S2I - An estimate of precursor purity.

P2T - An estimate of precursor signal-to-noise.

T2APEX_sec - An estimate of the time (in seconds) between the MS/MS and the precursor apex (in seconds, where positive values correspond to MS/MS scans taken post apex).

FWHM_sec - An estimate of the peak width (in seconds).

COMMENT - Highlights potential issues with the peak characterization.