To clarify, I am using Sorcerer (from Sage-N) located on a different drive. So, in order to take full advantage of TPP, I have to convert the .out files into a pep.xml file that can be read peptide prophet, inter prophet, and protein prophet. The problem I am having is then being able to view the Spectra in the interact.pep.xml viewer, since no where in original Sequest->TPP input did it specify a path for either the .dta or .mzXML file (it only asks for the .out files and a parameter file).
I have tried to manually incorporate a path to the mzXML in the interact.pep.xml by using: <msms_run_summary base_name="c:\Inetpub\wwwroot\ISB\data\EColi\e120823_EC_1uL\SorcererTests\Parametric" search_engine="Sequest" msManufacturer="Thermo Scientific" msModel="LTQ Orbitrap Elite" msIonization="nanoelectrospray" msMassAnalyzer="radial ejection linear ion trap" msDetector="electron multiplier" raw_data_type="raw" raw_data=".mzXML"> <parameter name="spectrum, path" value="c:\Inetpub\wwwroot\ISB\data\EColi\e120823_EC_1uL\SorcererTests\Parametric\e120823DC_EC_04.mzXML"/> (My hope in doing this is to be able to combine multiple analyses into a interact.iproph.pep.xml and be able to view the spectra there). Is there any way to manipulate the interact.pep.xml further so I can view the spectra? Thank you in advance -Chris McKennan On Monday, December 3, 2012 12:40:22 PM UTC-5, Chris McKennan wrote: > > Dear All, > I am a relatively new user to TPP and have been trying to convert Sequest > .out files to a .pep.xml file. In the Sequest Analysis Pipeline I have > options to load a directory containing all .out files and a .param file, > but no file containing scan times (i.e. a .dta or .mzXML). When TPP > completes my command, I receive a warning message in the output box that > says: "warning: cannot open mzXML file " " for reading MS instrument info > and scan times". Is there a way to load .dta files with their corresponding > .out files or use the command line to specify the path to the .mzXML file? > > Also, I find that TPP will not recognize zipped folders containing .out > files. Is there a way to input zipped .out files? > > Thank you in advance, > Chris McKennan > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/ezdC7aCrvj4J. 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.
