"Yes" to your question. On Tue, Jul 20, 2010 at 10:34 AM, tommyg <[email protected]> wrote: > 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. > >
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