You need to set the minimum peptide length to 0 to get the PeptideProphet to process Kojak results. Also you should consider setting minimum probability to 0 for the analysis (you can apply the stringent cutoff later) and also run iProphet on the data. Your results should improve.
-David On Fri, Jan 20, 2017 at 8:54 AM, Van Kelly <[email protected]> wrote: > I am running TPP5.0.0 on windows and doing Kojak searches. Search results > open in the PepXMLViewer and present crosslinked peptides without issues. > But when I run PeptideProphetParser (on the terminal, not using the GUI) it > fails, despite clearly being aware that the data is Kojak derived. Has > anyone else encountered this, or know of a solution to the problem? Output > below: > > > adding XLSecondScoreFraction mixture distribution > > init XL model with Kojak Trypsin > > init with Kojak Trypsin > > init Loop model with Kojak Trypsin > > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > > INFO: Processing xl MixtureModel ... > > PeptideProphet (TPP v5.0.0 Typhoon, Build 201610111222-7423 > (Windows_NT-x86_64)) AKeller@ISB > > read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > > read in no data > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
