Hi Robert, regarding the conversion of protXML and pepXML to mzIdentML, we rely on the idConvert tool. I’m very interested to hear how it didn’t work for you. Let’s chat about what you tried and how exactly it didn’t work and see if we can fix it.
Thanks, Eric *From:* [email protected] [mailto: [email protected]] *On Behalf Of *Robert Winkler *Sent:* Wednesday, July 27, 2016 3:08 PM *To:* [email protected] *Subject:* Re: [spctools-discuss] History of search_engine attributes in the pepXML schema/ mzid Hi Luis, how are you doing? I hope very well! When is TPP 5.0 coming? I would like to include it into MASSyPup64 to provide it "ready to use" for interested users. On the other side, I have some trouble to convert .prot.xml TPP outcome to .mzid -> it is not accepted by ProteomeXChange. Is there a trick? Best Regards, Robert On 27/07/16 17:00, Luis Mendoza wrote: This has been fixed in the new schema (pepXML_V120.xsd), which is already on our code repository, and scheduled to be released with TPP 5.0 soon. Cheers, --Luis On Thu, Mar 3, 2016 at 9:37 AM, David Shteynberg < [email protected]> wrote: Hello Mal, Your point seems valid to me. Getting the an old demo file to validate against the schema shouldn't warrant requiring this information to be present multiple times in the file. We will correct this problem for a future schema version. Thanks for your detailed report! -David On Thu, Mar 3, 2016 at 3:28 AM, Mal Ross <[email protected]> wrote: Hi there, I was just looking back through the history of the PepXML format <https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/schema/> and noticed that the latest commit shown for pepXML_v112.xsd mentions the removal of the search_engine attribute from the msms_run_summary element: https://sourceforge.net/p/sashimi/code/4028/ However, in pepXML_v118.xsd, I see that this attribute has returned in a commit that's aimed at getting a demo2009 file to validate: https://sourceforge.net/p/sashimi/code/6143/ Does that mean the attribute should never have been removed in the first place? It actually strikes me that it was *correct* to remove it and that the subsequent *reintroduction* is misguided, as child search_summary elements have their own search_engine attribute anyway. However, any guidance on this would be appreciated. Thanks, Mal. -- 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. -- 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.
