Dear David, Thank you for your reply and the offer to help!
I will answer in my original post to avoid spaming this announcement too much. Best regards, Juergen David Shteynberg schrieb am Donnerstag, 4. April 2024 um 17:15:02 UTC+2: > Now that I have also read your original message... sorry, I somehow missed > that message originally. I have used Lib2HTML to successfully convert a > spectral library to an HTML page, although I do remember having some issues > with unrecognized modifications when I first tried. Lib2HTML is a > completely separate tool from Seq2MS and uses a different code base. The > version of the Seq2MS software in the TPP is somewhat different from the > original version and includes more PTMs encoded. So this is still a bit of > a work in progress with the PTMs and I would be happy to help you further > if you can share your input files so I can reproduce the problem. Seq2MS > in the TPP distribution currently supports the subset of proforma mods > pasted below. > > Cheers! > > Oxidation Phospho TMT Silac Carbamyl Carbamidomethyl Acetyl Methyl > Hydroxylation GlyGly Biotinylation Crotonyl Dimethyl Malonyl Nitro > Butyryl Formyl Gluratylation hydroxyisobutyryl Propionyl Succinyl > Trimethyl Deamidated Gln->pyro-Glu Glu->pyro-Glu > > > > On Apr 4, 2024, at 6:59 AM, David Shteynberg <david.sh...@isbscience.org> > wrote: > > Hello Juergen, > > Thank you for your question and use of TPP! Seq2MS's support in TPP is > brand new. Truncation at the PTM usually indicates that the modification > was not recognized or encoded in the model you applied. Can you tell me > the model you applied and the modification you were searching? > > Thanks! > David > > On Thu, Apr 4, 2024, 2:19 AM 'Juergen Bartel' via spctools-discuss < > spctools...@googlegroups.com> wrote: > >> Dear TPP Team, >> >> Thanks for generating the new TPP version. Just a question concerning the >> release notes: These state that Seq2MS was added. Does that also mean that >> the issue I mentioned some time ago with Lib2HTML ([This topic] >> <https://groups.google.com/g/spctools-discuss/c/3Sa9QZXAWWU/m/qHZ4LEEOAQAJ>; >> when peptides with multiple different modification variants are present on >> the same residue, it did truncate the peptides after the modified residue) >> was solved? >> >> Best regards, >> Juergen >> >> >> >> David Shteynberg schrieb am Samstag, 30. März 2024 um 02:47:30 UTC+1: >> >>> Announcing the official release of Trans-Proteomic Pipeline (TPP) 7.0.0 >>> >> Arafel >>> >> >>> We are proud to offer a major update to the Trans-Proteomic Pipeline >>> (TPP) software, release 7.0.0. The software is available for MacOS, >>> Windows, Linux, as well as Android from all the usual locations (please see >>> the section below, >>> >> Getting the TPP Software >>> >> ). We recommend for most users to use the Windows or MacOS installer, >>> which installs and configures TPP and other required software, such as the >>> Apache web server, perl, and python. For advanced users, who need to >>> customize TPP, or for those users who run on Linux or Android, the source >>> code should be downloaded and the software configured and compiled. If >>> building from source, please add your site specific configuration to >>> site.mk in the top level directory after unpacking the source-code. >>> >>> == Highlights == >>> + MacOS two-click install! >>> + Python Support and addition of Seq2MS for Generative AI of Peptide >>> Fragment Spectra >>> + Native Support of Kojak for Cross-linked Peptide Search >>> + Native Support of Magnum for Open-mass Peptide Search >>> + StPeter Quantification >>> >> by run >>> >> or >>> >> by experiment >>> >> + Easy to access PeptideProphet VMC model for rare-PTMs >>> >>> >>> == Release Notes == >>> Release notes on the most important new features, changes, and known >>> issues are available at: >>> >>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.0.0_Release_Notes >>> >>> >>> == Getting the TPP Software == >>> Download the TPP version 7.0.0 native windows installer from the Sashimi >>> SourceForge project file release page: >>> https://sourceforge.net/projects/sashimi/files/latest/download >>> >>> Everyone is encouraged to read and contribute to our wiki, at >>> http://tools.proteomecenter.org/wiki/ >>> >>> For guides to installing and using our software, please see our wiki: >>> http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP >>> >>> For downloading the source code, please go to the following link: >>> http://sourceforge.net/projects/sashimi/files/ and find the 7.0.0 >>> source code package >>> or, check out the code directly from svn: >>> svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_7-0-0 >>> >>> For building from source, please refer to the README and INSTALL files >>> in top level source directory of the TPP code tree as well as the wiki. >>> >>> >>> == Acknowledgements == >>> The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers >>> who contributed to this release from ISB. Thanks to developers and users >>> from the TPP's user community who also provided feedback and code >>> contributions. >>> >> >> -- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/1c67b759-658f-45bd-8533-455c7248c299n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/1c67b759-658f-45bd-8533-455c7248c299n%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 spctools-discuss+unsubscr...@googlegroups.com. 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