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Manual

The following guide will allow you to visualize protein/peptide data with Proteator. Begin with Uploading data in order to learn how to map peptides to their respective positions on the protein. Tools and filters provides information for the different tools or filters to use.
For usage of Proteator, we recommend the web browser Google Chrome, although some other browsers will also work. Please note that Proteator is still under development and will receive updates from time to time which will improve its functionality.

Uploading data


  • Download example files: .txt file (use this file to test the input of custom files) or .mzTab file

  • Procedure for using custom files:
  • Requirements: The required input consists of at least one text file, e.g. .csv or .tsv files. When using other file types, please make sure they contain protein identifiers (e.g. P12830) and the sequence of identified peptides (e.g. K.n[1.01]YTALVDQEEKEDVKc[17.00].S). The header for the respective columns should be located in the first line of the text file.
  • Under Files select any number of files that you want to visualize. Please note that big or many files will increase loading time.
  • After all files have been selected, press submit.
  • The following window will open up:
  • At the upper left corner, the file names are displayed. Click on the names to change the active file.
  • The table in the center of the window provides a preview of the file.
  • Please enter the following information:
  • Note for TPP-XPress: If you have several files, one of which containing xpress ratios, the other one the peptides, check in the file with the peptides the box "only use ratios". All xpress ratios will be retrieved from this file by the sequences of the peptides specified in the other file.

  • Procedure for using .mzTab files:
  • Proteins that should be displayed must be specified in the PRT section of the .mzTab file. Peptides should be listed in the PSM or PEP section
  • Select one or several .mzTab files and press submit.
  • For visualizing express ratios with .mzTab files, at least two "peptide_abundance_study_variable" columns must be present. In the input window you can specify the respective column for treatment and control.

  • Proteator will now begin downloading the necessary protein data from Uniprot. The progress can be followed by the appearance of the following progress bar:
  • Please be patient as the download can take some time.
  • Once it is finished, the submitted data will be displayed in the following form:
  • Accession and long name of the protein are displayed on the top left. Click on the accession to be redirected to the protein entry on Uniprot.
  • It follows a scale for the size of the protein and the protein itself. The colored areas on the protein correspond to certain topological domains. Refer to the legend on the right or hover your mouse over the protein to learn which color means which type of domain.
  • Below the protein you can see the peptides mapped to it. If an express ratio was entered during input, the fold change will be calculated and reflected by the color of the peptide. Peptides without express ratio will be displayed in black. The exact number will be listed as foldchange - log2(xpress) - on the bar below the protein. Hover your mouse over a peptide or click on it to see its sequence and express ratio.
  • Click on the "+" button for a more extensive view of the protein sequence with mapped peptides and topological annotation.
  • Tools and filters

    Settings:

    Filters:

    Tools:

    Impressum

    Proteator was created by Patrick Heisterkamp (contact: patrick.heisterkamp@gmail.com), University of Freiburg, for the AG Schilling, University of Freiburg.
    Especial gratitude goes to Lars Nilse and Björn Grüning (both University of Freiburg) who provided valuable support during the development.
    The sequence viewer is used under Apache License 2.0. It was created by greenify and ljgarcia on biojs.io.

    Publication:
    Lars Nilsea, Dönem Avcib, Patrick Heisterkampa, Oliver Serangc, Marius K. Lembergb, Oliver Schilling
    Yeast membrane proteomics using leucine metabolic labelling: Bioinformatic data processing and exemplary application to the ER-intramembrane protease Ypf1
    BBA-Proteins Proteom., 10 (2016), pp. 1363-1371

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