Aah. No, there were no msLevel=2 entries, while in all the other files there are ones that are searched by Tandem. I am quite new to this--does that mean that for this particular file the actual experiment was not run as tandem ms?
Thanks, Tom On Jul 20, 10:17 am, Jimmy Eng <[email protected]> wrote: > 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 > > 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.
