Dear Robert, thank you for sharing this with everyone, this looks like a great resource. The maintenance of a resource like this is important, and it is really great that you've been maintaining and updating this for quite a long time now!
Regards, Eric -----Original Message----- From: spctools-discuss@googlegroups.com [mailto:spctools-discuss@googlegroups.com] On Behalf Of Robert Winkler Sent: Tuesday, November 17, 2015 1:35 PM To: spctools-discuss@googlegroups.com Subject: [spctools-discuss] "TPPish" taverna workflow with text mining/ Association analyses for peptides Dear TPP friends, I just published a quite extensive open access article about advanced mass spectrometry data analysis: (An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64, https://peerj.com/articles/1401/). It contains an example for the peptide/protein identification with comet/PeptideProphet/ProteinProphet, with subsequent export of the results in various formats (Excel, csv, html) and extraction of hits relevant for the project (e.g. protein names containing "peroxidase"). Running the TPP/ textmining taverna workflow only requires 1) revising/ adjusting the comet.params file (with location of the fasta sequence DB), 2) defining the .mzML data directory and 3) defining the text search term for the results (if required). Further parameters may be adjusted, if desired. Importantly, the data do not have to be moved to a certain directory (such as /wwwdata), but are processed where they are ("in place"). Technically speaking, the workflow is constructed with taverna (http://www.taverna.org.uk/), employing the TPP scripts (4.8), comet (http://sourceforge.net/projects/comet-ms/) and standard linux commands (grep, ..). The complete workflow (with dependencies and example data) runs straight away from the latest release of MASSyPup64, http://www.bioprocess.org/massypup/. The workflow file is attached to this email (I hope it arrives, if not, please tell me). The article also demonstrates, how an Association Analysis of the peptide hits can be performed with Rattle. This Data Mining strategy is useful, to detect co- occurring peptides (i.e. with low frequency, but high confidentiality), e.g. when looking for alternative biomarkers. The strategy is well known from Market Basket algorithms ("maybe you also want to buy Parry Hotter 2-8?") and Social Networks ("do you know Peter, Paul and Marry?") .. Any comments are welcome! Best regards, Robert -- Este mensaje ha sido analizado por MailScanner en busca de virus y otros contenidos peligrosos, y se considera que está limpio. For all your IT requirements visit: http://www.transtec.co.uk -- 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 http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
