Hi David, I had some discussion with Brian off list. It seems like there are some parts missing from the pepxml file
To continue here: As a test I started the peptide prophet from the command line to analyse 2 HPL runs from 1 independent experiments (in the end 8 HPLC runs from 4 experiments): C:\Inetpub\tpp-bin>xinteract -Nc:/Inetpub/wwwroot/ISB/data/Sabine/ Gruss/08-094u129TPP42r1/test_experiment/new_exp1_interact.pep.xml - Eexp1 -p0.05 -l7 -Ol -X-m0.01-nK,6.0204-H-F35 -A-lK-F-r0.003 c:/ Inetpub/wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/ test_experiment/08-094-04.pep.xml c:/Inetpub/wwwroot/ISB/data/Sabine/ Gruss/08-094u129TPP42r1/test_experiment/08-094-05.pep.xml Afterwards I started iprophet from the gui: run_in c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/ test_experiment; InterProphetParser c:/Inetpub/wwwroot/ISB/data/ Sabine/Gruss/08-094u129TPP42r1/test_experiment/ new_exp1_interact.pep.xml c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/ 08-094u129TPP42r1/test_experiment/new_exp2_interact.pep.xml c:/Inetpub/ wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/test_experiment/ new_exp3_interact.pep.xml c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/ 08-094u129TPP42r1/test_experiment/new_exp4_interact.pep.xml new_exp1234_interact.iproph.pep.xml and finaly I started proteinprophet from the gui: c:/Inetpub/wwwroot/ISB/data/Sabine/Gruss/08-094u129TPP42r1/ test_experiment/new_exp1234_interact.iproph.pep.xml c:/Inetpub/wwwroot/ ISB/data/Sabine/Gruss/08-094u129TPP42r1/test_experiment/ new_exp1234_iprophet_interact.prot.xml XPRESS ASAP_PROPHET A folder (TPP-files ZMBH.zip) containing the following files is uploaded: one of the 8 mzML files one of the 8 pep.xml after Mascot search (separate search with Mascot daemon) one of the 4 peptide prophet files interact.pep.xml the .iproph.pep.xml the interact.prot.xml with the iproph.pep.xml as input Thanks, Thomas --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
