Thanks Matt mscat looks spot on for what I need, sorry for the confusion, that should have read
"has the data for all the scans like mzml" I'm only interested in scan number, m/z and intensity for this extract Cheers Chris On Nov 28, 3:35 pm, Matthew Chambers <[email protected]> wrote: > 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- 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.
