Hi Chris,
mscat may do what you want - just redirect its output to a file. If you only want MS1s, you'll have
to create an intermediate mzML/mz5 first. However, this certainly will not achieve your original
metadata requirements:
"has all the scan data like the mzml"
For that, you might try msconvert --text which will show the mzML data model in its tree structure,
including binary data. And msconvert can use the ms level filter directly.
-Matt
On 11/26/2011 1:54 AM, Chris wrote:
Thanks for the reply, Eric
Of course, I forgot it's the thanksgiving break.
So I'm looking for either a modified mgf extract that gives me all
scans or a whole new format that will do the same job.
Chris
On Nov 25, 4:09 pm, Eric Deutsch<[email protected]> wrote:
Hi Chris, MGF files are by definition designed for MS2 spectra, with no
MS1 spectra, so msconvert is doing the right thing. I am not aware of a
plain text format for encoding MS1 data that msconvert supports, but I am
not familiar enough with msconvert to really know. We'll have to wait for
a response from the protoeowizard folks. But it's a holiday in the US so
it might not come for a while.
Regards,
Eric
-----Original Message-----
From: [email protected] [mailto:spctools-
[email protected]] On Behalf Of Chris
Sent: Friday, November 25, 2011 3:46 AM
To: spctools-discuss
Subject: [spctools-discuss] Scan Levels in MGF Files
Hi All
Sorry if this is a noob question, I'm looking at Mass Spec. data from
an IT/database point of view and am struggling a little with the
specific terms which may well mean the answer I want is already here
somewhere - I just can't find it!!!
So, if I take a file from a Thermo Mass Spec and convert it to mzml
using msconvert, I get all the scans and all the data from the RAW
file.
If i take the same file and use msconvert to create a MGF file, I
appear to get level 2 scans only
running a command with the switch as below, the resulting file is
empty
--filter "msLevel 1"
Is this by design? I want a file that looks like the MGF but has all
the scan data like the mzml
All help and guidance, much appreciated unless it's RTFM because I've
tried that :-)
Cheers
Chris
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en.
