Look for or do a string search for the text: msLevel="2" These are the ms/ms scans that would be searched by Tandem.
On Tue, Jul 20, 2010 at 10:04 AM, tommyg <[email protected]> wrote: > Hi Jim, > The mzXML file is about 290 mb and has many scan entries that look > like other mzXML scan entries from files that I was able to run. There > are 19517 scans in this particular file. I copied an example of a scan > entry. Is there something else I should look for to confirm there are > ms/ms scans? > > <scan num="19517" > scanEvent="1" > scanType="FULL" > centroided="1" > msLevel="1" > peaksCount="56" > polarity="+" > retentionTime="PT3000S" > lowMz="400.1986083984375" > highMz="1122.22021484375" > basePeakMz="444.97515869140625" > basePeakIntensity="1593.150634765625" > totIonCurrent="16308.9521484375" > msInstrumentID="IC1"> > <peaks precision="64" > byteOrder="network" > pairOrder="m/z- > int">QHkDLYAAAABAUJxTgAAAAEB5RSjAAAAAQGgNbsAAAABAeVGLoAAAAEB1MZpAAAAAQHlmL4AAAABAezhpwAAAAEB5diBAAAAAQE60nWAAAABAeYODYAAAAEBiiDRAAAAAQHm7j2AAAABAdWpfQAAAAEB50oBgAAAAQFo8CIAAAABAegAA4AAAAEBjqfxAAAAAQHowO > +AAAABAfEVDIAAAAEB6Qa3AAAAAQFgOiSAAAABAemQ34AAAAEBkuQYAAAAAQHpzaUAAAABAU7N4YAAAAEB6nILgAAAAQF6QP4AAAABAez3lAAAAAEBRiknAAAAAQHttS4AAAABAWkAfwAAAAEB7tBXgAAAAQFxqm8AAAABAe8+aQAAAAECY5JpAAAAAQHvfvWAAAABAgTuT4AAAAEB78M8AAAAAQJiPG0AAAABAfADHQAAAAEB491fAAAAAQHwTYeAAAABAUaiuIAAAAEB8vkUgAAAAQGXQEWAAAABAfMjToAAAAEBhcqpgAAAAQHzfGmAAAABAd > +U1QAAAAEB9T6RAAAAAQFgN/ > YAAAABAfbTBgAAAAEBm8pugAAAAQH3jvCAAAABAU7bDoAAAAEB/ > jrbAAAAAQFpBIkAAAABAf6+sQAAAAEBTt3CAAAAAQIA3s > +AAAABAlC9QwAAAAECAP4jAAAAAQJGW5eAAAABAgEc8AAAAAEBtaqVAAAAAQIBPsIAAAABAY6MpQAAAAECAqPwgAAAAQFgB0KAAAABAgoZ2QAAAAECJzGQgAAAAQIKPLgAAAABAgZ/ > ZIAAAAECClyrAAAAAQHzKF2AAAABAgp9D4AAAAEBaPRcAAAAAQIMX/ > kAAAABAWFEIIAAAAECE0teAAAAAQHZgxqAAAABAhOFzgAAAAEBusFlAAAAAQITnvYAAAABAaieu4AAAAECE9cWAAAAAQFXg6mAAAABAhx2egAAAAEBV2+iAAAAAQIcmRYAAAABAhJ9RoAAAAECHLfDAAAAAQGoudEAAAABAh0UUoAAAAEBWAzyAAAAAQIdbKcAAAABAWjoogAAAAECJdC4AAAAAQHQtpoAAAABAiYTRwAAAAEBaPJSgAAAAQImdxoAAAABAVeIAYAAAAECKFzbAAAAAQEpqGOAAAABAi9YBoAAAAEBRuA3AAAAAQJA/ > PiAAAABAWjof4AAAAECRiOGAAAAAQFO1l8AAAAA=</peaks> > </scan> > > > > On Jul 20, 9:53 am, Jimmy Eng <[email protected]> wrote: >> Tom, possible there are no ms/ms scans in this raw file? >> >> On Mon, Jul 19, 2010 at 2:01 PM, tommyg <[email protected]> wrote: >> > Hello, >> >> > I'm getting a "No input spectra met the acceptance criteria" error >> > while running the latest version of X!Tandem on a 64-bit Intel(R) >> > Core(TM)2 Duo CPU E6550 @ 2.33GHz running Fedora 11. >> >> > I've successfully run many other .pkl files, but for this >> > particular .RAW file (D2.raw), I was not able to convert it to a .pkl. >> > I was able to convert it to D2.mzXML or D2.mzML file using TPP/ >> > msconvert, but still getting the error when running XTandem on these >> > files. Additionally, I cannot convert the mzXML to pkl (or any other >> > format) using MzXML2Search. >> >> > I was able to convert other .raw files to mzXML, and then to pkl, and >> > I was able to run these files successfully on XTandem. So this is >> > specific to this one particular D2.raw/D2.mzXML file.It appears that >> > there are spectra. Any ideas? >> > I can upload the mzXML file if it would help. >> >> > Thanks, >> > Tom >> >> > -- >> > 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 >> > athttp://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. > > -- 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.
