Thank you for following up. On Oct 23, 2017 8:34 PM, "Adam R" <[email protected]> wrote:
> Hi David, > > Just wanted to confirm that I had success with the patch that you > provided. Thanks again! > > Best, > > Adam > > > On Monday, October 23, 2017 at 4:35:20 PM UTC-5, David Shteynberg wrote: >> >> Hi Adam, >> >> Thanks for submitting the bug report. I have traced it to a problem with >> iProphet processing small files. I have corrected the issue and have a >> patch here: https://www.dropbox.com/s/mq9yv5a4ew9umhe/InterProphe >> tParser.exe?dl=0 >> >> Please replace your existing copy in C:\TPP\bin\InterProphetParser.exe >> with the one from my patch and try again. >> >> Cheers, >> -David >> >> On Mon, Oct 23, 2017 at 12:51 PM, Adam R <[email protected]> wrote: >> >>> Hi David, >>> >>> I have attached a screenshot of the parameters used, and have also >>> attached screenshots of the output of the command. I figure there are a few >>> abundant peptides that should make it through iProphet... >>> >>> Best, >>> >>> Adam >>> >>> >>> >>> On Monday, October 23, 2017 at 1:51:08 PM UTC-5, David Shteynberg wrote: >>>> >>>> I have run the TPP on MSFragger results, including iProphet, before. >>>> What parameters did you use for PeptideProphet? What was the output of >>>> that command? Is it possible that you don't have any high scoring PSM left >>>> after PeptideProphet filtering? >>>> >>>> Thanks, >>>> -David >>>> >>>> On Mon, Oct 23, 2017 at 11:42 AM, Adam R <[email protected]> wrote: >>>> >>>>> Hi Everyone, >>>>> >>>>> I am running into a problem with iProphet when trying to perform >>>>> additional validation on PeptideProphet files sourced from MSFragger >>>>> pep.xml output. The command fails and >>>>> shows the warning "file not found: not created or deleted?" Has anyone >>>>> else had this issue before? I would like to be able to use MSFragger >>>>> output >>>>> files (wide mass search) and feed the resulting output through >>>>> PeptideProphet/iProphet/PTMProphet. >>>>> >>>>> Thanks, >>>>> >>>>> Adam >>>>> >>>>> >>>>> -- >>>>> 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. >>> >> >> -- > 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.
