Converting Thermo (LTQ velos) to mzXML -> adding precursor charges

[Robert]

Hi,

when converting Thermo (LTQ velos) raw files to mzXML, no precursor
charges are included in the resulting mzXML. I tried ReAdW (TPP) and
msconvert (Proteowizzard).

This is not a problem for X!Tandem searches, but for some uses
(calculation of mass errors, PRIDE XML repository), the precursor
charge would be desirable.

Any suggestions, how the charge could be added to mzXML?

Best, Robert

[Greg Bowersock]

Precursor charge is already in mzXML. If you look at the mzXML files created by ReAdW (msconvert should also have it), you should see lines such as:

<precursorMz precursorIntensity="2123.5" precursorCharge="4" activationMethod="CID" >1390.82</precursorMz>

Those lines are part of the msms scan information (ms level = 2). If the line isn't there, you might want to check the method on LTQ to make sure that Charge State Screening is enabled for the segment in the dependent scan settings.

Greg

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[Jimmy Eng]

Greg, the precursorCharge attribute is only present for data where the
charge state is present in the raw file. This usually is true for
FT/Orbi data but not normally with LTQ/Velos data.

Robert, the real question is what precursor charge would you want to
be associated with each ms/ms spectrum for your LTQ Velos spectra?
Since there's no precursor charge in the underlying RAW file, the
converters won't make them up. It's not inconceivable to implement
charge state guessing rules, like those implemented in Tandem, but I'm
not sure this is going to happen for many reasons.

[Matthew Chambers]

The chargeStatePredictor filter in msconvert will do the standard single/multiple guessing or ETDZ
prediction for ETD MSn spectra. I.e. --filter "chargeStatePredictor false 3 2 0.9"

-Matt

[LW]

Hi Matt, how about for CID spectra? Is there charge prediction available?

-LW