Hi, I am the developer and maintainer of massypup64, a live system for data analysis, workflow creation and data mining of mass spectrometry data (http://www.bioprocess.org/massypup/). One of the example workflows on the system analyses mzML files with comet (target-decoy) and following performs a hit validation with the TPP Prophet scripts. The workflow is set up in taverna and creates output in various file formats (for details: https://peerj.com/articles/1401/). Unfortunately, the mzid files are not recognized as result files in ProteomeXChange submission. Any idea, how to generate a valid mzid file from the mzML, pep.xml, prot.xml, fasta files? Ideally, with a command line program/ script (bash, python, Perl, java, R,.. Open Source).
Thanks, Robert
Hi Dr Robert,
For aminoacids aligning, I´ve used the NCBI website. However, Dr Luis Delaye is using a step by step sequencing software based in Prophet. Would please contact Dr delaye for details?
I found this information. Perhaps it might help you with something.
http://www.bioconductor.org/help/workflows/proteomics/
Regards
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