I have not yet created a container for 6 but I should. I could try to do that soon if there is demand to use it/test it.
Thanks, Eric *From:* 'Alastair Skeffington' via spctools-discuss < [email protected]> *Sent:* Monday, June 21, 2021 8:59 AM *To:* spctools-discuss <[email protected]> *Subject:* Re: [spctools-discuss] tpp2mzid help - 'no peptide evidence found ...' Hi Mike, Thanks for getting back to me so quickly. Here's the database: https://we.tl/t-wZsZ3uSq1r Is version 6 available as a container? I've never managed to install TPP properly on a linux machine ... Alastair On Monday, 21 June 2021 at 17:50:24 UTC+2 [email protected] wrote: Hi Alastair, There is a much newer version of tpp2mzid in our current release candidates of TPP version 6. I’m hoping that the error messages have been resolved in this new version. However, I also need the fasta search database file to run the conversion with the newer tpp2mzid. Could you also provide a link to that file and I will finish my tests and let you know the result? Thanks, Mike *From:* 'Alastair Skeffington' via spctools-discuss < [email protected]> *Sent:* Monday, June 21, 2021 6:45 AM *To:* spctools-discuss <[email protected]> *Subject:* [spctools-discuss] tpp2mzid help - 'no peptide evidence found ...' I'm at the end of a multi-year odyssey of a project, and I just need to submit data to PRIDE. Unfortunately, when I run tpp2mzid for some prot.xml files, I get an error such as this: Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from Br20418.t2 This only happens for some prot.xml files, but I'm not sure why. The pep.xml files from which the prot.xml are derived convert fine. I've put an example here: https://we.tl/t-Z9qNNjDC0k I was running TPP via the docker container: digitalproteomes/tpp:version-5.2.0.1 Here is the stdout in full: Reading: HCLC_EhN.prot.xml Reading: /data/HCLC_EhN_ipro.pep.xml Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 Unknown xx modification: B = 114.535 42.5515 Unknown xx modification: J = 113.084 44.0023 Unknown xx modification: O = 237.148 80.0613 Unknown xx modification: U = 150.954 6.13277 Unknown xx modification: X = 111 46.0864 Unknown xx modification: Z = 128.551 28.5358 17648 psms read. Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from Br20418.t2 Help would be very much appreciated! Thanks, Alastair -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f3791dbe-d3d4-43cf-aeda-65792741656fn%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/f3791dbe-d3d4-43cf-aeda-65792741656fn%40googlegroups.com?utm_medium=email&utm_source=footer> . -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/15675077-97af-476e-b471-d6315c5ec078n%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/15675077-97af-476e-b471-d6315c5ec078n%40googlegroups.com?utm_medium=email&utm_source=footer> . -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/620529cb2cb808d958bff329305a3608%40mail.gmail.com.
