ETD/CID inclusion list

ETD/CID inclusion list read a table of peptides sequences with post translational modifications (PTM) mass shifts and retention times (RT) and calculate peptides masses and charges states with the corresponding inclusion list for scheduled precursor analysis by mass spectrometry.

Manual :

1- install Julia free programming language and install package :

DataFrames : Pkg.add("DataFrames")

2- unzip the software.

3- edit config file in the config directory and enter the values for :

# maximal number of charges in calculated m/z

zmax=5

# mass tolerance in dalton

detaMZ=0.6

4- copy your n tables in csv (TAB delimitated by default) files in the “data” directory.

- first line of the table : column names (sequence mass_shift RT_min DeltaT_min)

- next lines : values

The final peptide mass = peptide mass + PTM

DeltaT is the time tolerance in minutes for the peptide RT

example :

5- execute the software by the command : julia software_name

6- results tables are in the results directory. Inclusion lists are in the list directory.

The format of the inclusion list is :

Time +/-Time Tolerance Mass Begin Mass End

Times are expressed in second in the inclusion list and in minutes in the data table