Re: [proteowizard-support] DIFFERENCES BETWEEN .MGF AND .MZXML DATA FILES

[Darren K. <da...@pr...>]

Hi Patrick,

I can comment on #2, and I'll refer you to Matt Chambers, another
ProteoWizard developer, about #1.  Matt, please see below for a
question regarding MGF format.

The size differences between the files generated by msconvert and
ReAdW should be due to differences in the metadata.  The actual
base64-encoded scan data should be the same.  Note however that  we
have an option for 64-bit vs 32-bit encoding (and I think ReAdW does
too), so you want to make sure that you're comparing files with the
same encoding.


Darren


On Wed, Apr 15, 2009 at 7:40 AM, Patrick Njuguna <pnj...@i-...> wrote:
> 14 – 04 – 2009.
>
>
>
> The ProteoWizard Team,
>
> The Spielberg Family Center for Applied Proteomics,
>
>
>
> Dear Darren,
>
> RE: DIFFERENCES BETWEEN .MGF AND .MZXML DATA FILES.
>
> We are building a solution for the proteomics community and are currently
> supporting the conversion of .RAW files into the .mzXML format using the
> ReAdW.exe tool from the Seattle Proteome Center. In a bid to improve our
> solution we would like to support more conversion formats for example .mzml
> and .mgf.  We were referred to the download page at sourceforge and
> downloaded your solution and have been testing it and have noticed the
> following.
>
> 1.       When we run msconvert from the command line and convert a file into
> the .mgf format the resultant file is always smaller than the resultant
> .mzXML file. What causes this huge difference in the sizes of these files?
> Our assumption is that the .mzXML format is written with a lot of
> descriptive tags which blow up the size which is not included in the .mgf
> file formats. Are we correct? Of greatest concern is loss of data when the
> .raw files are converted to these formats is there data loss when a file is
> converted to .mgf rather than .mzXML?
>
> 2.       There are differing sizes in the .mzXML files generated by
> msConvert.exe and ReAdW.exe is there any reason for this size difference?
>
> Kind regards,
>
>
>
> Patrick Njogu.
>
>
>
>
>
> ===================================================================
>
> Patrick Njuguna Njogu
>
> Systems Engineer
>
> Integrated Analysis, Inc.
>
> “Providing Meaning to Data” TM
>
>
>
> Email: pnj...@i-...
>
> ===================================================================
>
>