I would not recommend using the 0.05% cutoff. I was able to open your file and apply same filters you applied. I am using Firefox browser. Which version of the TPP are you using?
Thanks, -David On Fri, Aug 31, 2018 at 3:33 PM, Adam Rabalski <rabal...@gmail.com> wrote: > Hi David, > > Yes this is the file. Briefly, I would open it and after a few minutes > once loaded in Chrome I filter using an iProphet cutoff of 0.7360 and a > text filter for 478.99|480.99 modification (subscript checked on). Trying > to display all entries, or attempting to export to a spreadsheet results in > the error warning. I'm running another analysis currently with a 0.05 > cutoff. What browser are you using? > > Best, > > Adam > > On Friday, August 31, 2018 at 5:25:27 PM UTC-5, David Shteynberg wrote: >> >> Hello Adam, >> >> I have not been able to replicate the issue you observed on the file you >> gave me. Are you sure that the file you posted is the one showing up with >> the error? >> >> Thanks, >> -David >> >> On Fri, Aug 31, 2018 at 2:03 PM, Adam Rabalski <raba...@gmail.com> wrote: >> >>> Considering the size of the file, which editors/viewers do you use at >>> ISB to open XML file in order to pinpoint a problem? I have re-run the >>> analysis as I had 87 fractions and 10 of them were labelled with timestamps >>> (occurs when XCalibur attempts to write a filename that already exists in a >>> directory so it creates a new file with the date/time added on to it) so I >>> changed these file names as I thought that this might be the problem >>> because I could not view peptides beyond this fraction number but am still >>> running into the same issue and have different "error with html display" >>> pointing to different lines depending on how I filter the xml file. Would >>> reducing the output size help here? The only thing that I can think of >>> doing is increasing the PeptideProphet Probability filter to 0.05 from 0.00 >>> (which I typically use) in order to reduce the number of entries written . >>> >>> On Thursday, August 30, 2018 at 1:03:24 PM UTC-5, David Shteynberg wrote: >>> >>>> The errors above suggest that the pepXML files are not parser compliant >>>> and cannot be read. Sometimes this could be caused by bad characters in >>>> the protein descriptions from the fasta database, you have to look at the >>>> specific lines pointed to by the error messages to identify the exact >>>> issue. If you can post your failing files and I can take a look. >>>> >>>> Thanks, >>>> -David >>>> >>> -- >>> 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 spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
