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Special characters in file names often can cause problems further down the line, e.g. processing the files, listing the files on the website and web service, listing files for FTP/Aspera download. Thi…
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if an DBSequence element has a protein sequence then the sequence is read in and a right-sized circle represent the protein. But if only the length attribute is given the protein is represented by sin…
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Looks like currently decoys are not recognised when read in from an mzIdentML-file.
The file I uploaded had peptideevidences marked as decoy but all matches where displayed and none marked as decoy.
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Hi dear Harald,
I tried to parse the mzid file produced by PeptideShaker v.1.16.42 from my .cpsx file with the R package "mzID" but it reports some failure that are caused by the non-standard structu…
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the matches are not sorted by score
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as xiNET at crosslinkviewer.org does
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Working on RNA mass spectrometry, one problem is that there is no file format for storing oligonucleotide identification results. We have an experimental tool for doing database searching of MS2 spect…
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Hi everyone!
I have a problem with handling protein information in idXML file. Here is an example of a protein hit:
In the pyOpenms documentation I've found that the accession, the score a…
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In the output mzID file of MetaMorpheus, the names of some modifications are "unknown modification". But as shown below, they are present in UNIMOD so there should have names defined in UNIMOD for the…
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A complete PRIDE submission requires `mzML`, `mgf` and `mzIdentML`. We generated `mgf` with `FileConverter` and `mzIdentML` with a standard MS-GF+ workflow. The complete PRIDE submission is not possib…