An open-source framework for mass spectrometry and TOPP – The OpenMS Proteomics Pipeline




Protein-RNA cross-linking tools and workflows.


Download sample data and TOPPAS workflows:

RNPxl samples and pipelines
Please note that RNPxl_sample_UV.mzML and RNPxl_sample_control.mzML only contain a portion of a full experiment and have already been picked to reduce the size of the file.

Download the Win64 installer from:
Win64 installer



Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
Katharina Kramer, Timo Sachsenberg, Benedikt M Beckmann, Saadia Qamar, Kum-Loong Boon, Matthias W Hentze, Oliver Kohlbacher, Henning Urlaub
Nature methods



  • RNPxl crashes with error message indicating that an idXML was not found:
  • Error: File not found (the file 'C:/Users/username/AppData/Local/Temp/MSfilename_Number_Number_variant.idXML' could not be found)
    RNPxl failed!

    Omssa has problems reading the path to the database.
    Check that the path to your database or windows temp directory doesn’t contain any spaces or additional dots.
    Make sure that all database related files (.fasta, .phr, .pin, .psq) are in the same folder and have the same name that you defined both in the parameters of the RNPxl tool and the OMSSA .ini file.
    Also make sure there is no dot except for the one between file name and file type, e.g., do not call the database “uniprot.human.fasta”

  • Can you provide some details on the mass and losses of 4-thio-U nucleotide?
    The monoisotopic mass of a 4-thio-U nucleotide is: 340.01301 (C9H13N2O8PS).
    However, a net loss of H2S has always been observed in our cross-linking experiments, making the adduct mass: 306.02529 (C9H11N2O8P). This adduct is observed on precursor level. Fragmentation cleaves off phosphate and ribose, leaving 94.01671 (C4H2N2O) as adduct on MS2 level.