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. -- 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.
