[proteowizard-developer] mzXML's precursorCharge as a float

[Robert B. <rob...@pr...>]

Hello everyone,

This bug has been breaking our data pipeline, and I've tried to fix it
but have failed. So, I'm sending it to you. The summary is that under
some circumstances, msconvert is writing out precursorMz's attribute
precursorCharge with a decimal po
int. This is breaking Q3 searches, since they expect an integer (per
mzXML specification) and throw a format exception. I'm currently using
the windows and linux download from the site (3214).

The process is the following:

1) Files are converted from Thermo RAW to mzXML via msconvert on a
Windows XP box and place on the netowork. At this point, the
precursorCharge's are all integers.  The command line used is:
    msconvert --32 --mzXML <infile mask>
2) The resulting files are then filtered with precursorRecalculation
and stripIT. At this point, the precursorCharge's are written as
floats.


I can provide example files via dropbox.

A quick fix would be most welcome.

Thanks,
-RB