msconvert error

[WB]

Hi,
Does anyone know what's the problem below?
$./msconvert --spectrumrecords test_sort.mgf
[msconvert] No files specified.
[msconvert] no files found matching "test_sort.mgf"

Best regards!

BW

[Bill Noble]

msconvert is not part of Crux; it is part of Proteowizard.  You might try emailing their technical support:

http://proteowizard.sourceforge.net/contact.shtml


Cheers.
Bill

[WB]

Hi Bill:
When I use Tide(http://noble.gs.washington.edu/proj/tide/index.html),
it must use msconvert to format the mgf data to spectrumrecords format
data.
Can you convert mgf data to spectrumrecords format data successfully
by msconvert ?

Best
BW

[Benjamin Diament]

Hi WB,

As Bill mentioned in his reply, msconvert is part of proteowizard, but
the version you are using is a specialized version that can convert
into a format usable by Tide. Bill's answer is right in the sense that
msconvert is most probably reporting an error in the part of the code
that is unrelated to Tide.

I would try the following to troubleshoot the problem:

1. Be sure that test_sort.mgf is a readable, correctly formatted file.
I think the sort of error you got is the same you'd get if the file
were nonexistent, unreadable, blank, corrupted, contained no usable
spectra, etc.

2. Try using Tide's msconvert to convert test_sort.mgf to another
type, such as --mzXML instead of --spectrumrecords. This will
completely sidestep the Tide-related code and may give you some more
information.

3. If step 2 doesn't reproduce the problem, try a recent version of
msconvert from proteowizard to see whether a new version can convert
your file to another format (such as mzXML). It won't be able to do
--spectrumrecords, but you may get better error reporting regarding
your input file.

4. If the above steps only serve to confirm that your input file is
good, please repost with the results of the above steps.

Best,
Benjamin