Need help with MzXML2Search

[lgillet]

Hi,

I am running into trouble during the MzXML2Search export from mzXML to
mgf.

Here is what I observe:

- if you simply run "MzXML2Search -mgf file.mzXML", some scans do not
get
properly exported. I did not yet figure out the "rule" behind this
behavior, but this was particularly obvious to me since I was
expecting a set of specific 5+ or 6+ peptides.
I checked in the mzXML file and the expected precursor masses are
indeed there, and with the correct charge state properly assigned by
the mass spec instrument (QTOF). But those MS2 scans corresponding to
the precursors are clearly absent from the mgf.

- I found a message from another user in this list suggesting the
possibility to export specific charge states. So I run the command
"MzXML2Search -mgf -C2-6 file.mzXML", and while the first scans get
properly exported (you get the 2+, 3+, 4+, 5+, 6+ reports for each MS2
scan), the specific precursor I am looking for (scan=2643) gets
exported only as charge 1+, 2+, 3+, 4+?!?!?
Have somebody reported this before? Is there any option that I am not
aware of that could fix this issue?

I am happy to provide the mzXML file and specific example of set of
peptides that are not properly handled during the MzXML2Search export,
so that you may troubleshoot those by yourself.

Thanks in advance for your help with this. I really hope that will
help also other people too.

Best,

Ludovic

[Brian Pratt]

I'd be happy to have a look at it.  Just zip up the needed info and attach to a reply.

 

Brian Pratt

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[Jimmy Eng]

Ludovic,

Given that you're looking for 5+/6+ peptides, can you check to make
sure the peptide masses are not above the high mass cutoff default
(4200 Da) for MzXML2Search? If so, you would use the -T option to
specify a higher mass cutoff e.g. MzXML2Search -mgf -T8000.0
file.mzXML

- Jimmy

On Sun, Nov 22, 2009 at 11:50 PM, lgillet <gil...@imsb.biol.ethz.ch> wrote:

[lgillet]

Hi Brian, Hi Jimmy,


Thanks to both of you for your answers. Actually Jimmy was right: the
precursor was falling off the high mass cut-off.
Note that the -T option is not documented in the MzXML2Search options
(just when you run the "MzXML2Search" command to see the possible
options). Might be interesting to list it there too, for other people
that may encounter the same issues as I did.
But anyway thanks again for your quick reply and to have solved my
issues :)
Best,
Ludovic

[Brian Pratt]

FWIW, the -T option actually does get a mention in the usage statement,

" -T<num>      where num is a float specifying maximum MH+ scan, default=4200.0 Da"

although it refers to "maximum scan" instead of "maxmum mass", which may have caused your eye to trip over it.  I'll fix that.  Thanks for the pointer.

 

Brian

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[lgillet]

My mistake: I think I was too tired and I skipped that line.
Sorry for that and many thanks again for the tip and the solution to
my problems!
Best,
Ludovic

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