how to generate .mgf file from .mzXML

[chunchao]

Here is what I did. I generate a mzXML from Thermo RAW data using
ReAdW. Then I ran msconvert to try to get a mgf file from that mzXML
generated from RAW data (The command was: msconvert --.mzXML --.mgf;
also tried other ways like: msconvert --.mgf --.mzXML etc). But the
software always generate a mzML file instead of a mgf file. I don't
what's wrong with my conversion. Anyone has ideas? Thx!

[Jimmy Eng]

try something like: msconvert --mgf yourfile.mzXML

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[Matthew Chambers]

--mgf not --.mgf

[chunchao]

I tried this way but it failed too. Now I doubt if msconvert could do
that. Anyway, thx!


On Sep 14, 2:13 pm, Matthew Chambers <matt.chamber...@gmail.com>
wrote:

> > what's wrong with my conversion. Anyone has ideas? Thx!- Hide quoted text -
>
> - Show quoted text -

[Matthew Chambers]

Did you try Jimmy's command? Msconvert can certainly write MS2+ spectra to MGF.

-Matt

On 9/15/2010 10:14 AM, chunchao wrote:
> I tried this way but it failed too. Now I doubt if msconvert could do
> that. Anyway, thx!

[chunchao]

yes, I did.
For msconvert --mgf yourfile.mzXML, it says unkown option -m.

On Sep 15, 11:20 am, Matthew Chambers <matt.chamber...@gmail.com>
wrote:

[Matthew Chambers]

Are you sure you put two dashes? You will get that error if you only put one dash. If you're putting two dashes and still see that error, something very odd
is happening. If that's the case, what version of msconvert? Is it a non-English Windows? Are the localization settings set to something other than the default?

-Matt

[chunchao]

Definitely, 2 dashes. My OS is windows XP. I don't know the version of
msconvert because its already in cygwin.

On Sep 15, 3:50 pm, Matthew Chambers <matt.chamber...@gmail.com>
wrote:

> > For msconvert --mgf yourfile.mzXML, it says unkown option -m.- Hide quoted text -

[Matthew Chambers]

What do you mean "it's already in cygwin" ? Just run msconvert without arguments to get version information at the bottom. But I didn't even realize you were
running in cygwin. Did you try running it from the default cmd.exe prompt?

-Matt

[Amit Yadav]

You can directly convert thermo RAW files to mgf using msconvert. Why go through the trouble of converting to mzXML and then to mgf.

You can follow the thread's link below for more details. http://groups.google.com/group/spctools-discuss/browse_thread/thread/a5aae3bb8a79c20e/c9d36a54ea33a338?lnk=gst&q=msfilereader#c9d36a54ea33a338

Regards,

Amit Kumar Yadav 

Senior Research Fellow (SRF-CSIR)
IGIB, New Delhi (India)

MassWiz Web server

MassWiz sourceforge project

MassWiki

[chunchao]

I downloaded a newest TTP version and reinstalled on PC. This problem
was sovled. It looks like the previous version can't deal with this
problem. Thank you!

On Sep 15, 4:11 pm, Matthew Chambers <matt.chamber...@gmail.com>

wrote:
>   What do you mean "it's already in cygwin" ? Just run msconvert without arguments to get version information at the bottom. But I didn't even realize you were
> running in cygwin. Did you try running it from the default cmd.exe prompt?
>
> -Matt
>
> On 9/15/2010 3:07 PM, chunchao wrote:
>
>
>
> > Definitely, 2 dashes. My OS is windows XP. I don't know the version of
> > msconvert because its already in cygwin.
>
> > On Sep 15, 3:50 pm, Matthew Chambers<matt.chamber...@gmail.com>
> > wrote:
> >>    Are you sure you put two dashes? You will get that error if you only put one dash. If you're putting two dashes and still see that error, something very odd
> >> is happening. If that's the case, what version of msconvert? Is it a non-English Windows? Are the localization settings set to something other than the default?
>
> >> -Matt
>
> >> On 9/15/2010 2:36 PM, chunchao wrote:
>
> >>> yes, I did.
> >>> For msconvert --mgf yourfile.mzXML, it says unkown option -m.- Hide quoted text -

> >> - Show quoted text -- Hide quoted text -