Hi David, Just saw the results of the analysis with min PeptideProphet probabilty of 0.05 and I am now able to open the ptm.ipro.pep.xml file entirely with the filters applied. The resulting file is small (~ 375 MB) Export of the spreadsheet worked as well. This makes me think that this is likely an issue with file size on the system I am using (Windows Server 2012) I don't know what else could be the reason if you are able to open and apply filters to the xml file.
On the topic of the minimum PeptideProphet probability, during the summer course in Seattle in 2017 you mentioned during the tutorial session to drop this to 0.00 and it was related to keeping poorer scored spectra in order to have more data to model on in order to better learn from the decoy hits? This is my recollection, correct me here please. What is the difference between using 0.00 and 0.05 for min probability? I see a small reduction in the number of total modified peptides (down to 826 unique peptides now) but these could be from poorer scoring spectra anyways (I am now applying a iProphet filter of 0.7798 for a 0.01 error rate) 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 <[email protected] > <javascript:>> 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 [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
