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 spctools- > > [email protected]. > > For more options, visit this group at > >http://groups.google.com/group/spctools-discuss?hl=en.- Hide quoted text - > > - Show quoted text - -- 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.
