Chris, Try setting the "msms_run_summary base_name" and "search_summary base_name" to the name of the mzXML file. In your example below, have both "base_name=e120823DC_EC_04"and make sure e120823DC_EC_04.mzXML exists in the same directory as the interact.pep.xml.
See if that works to allow you to view the spectra. On Tue, Dec 4, 2012 at 10:09 AM, Chris McKennan <cg...@cornell.edu> wrote: > 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 > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
