Proteomics platform tools

List of proteomics tools

Example tools

• msconvert: tool to convert raw and standard ms format to standard ms format (open source tool from Proteowizard).
• peakaboo: peak picking tool for high resolution MS data (open source tool from Proteowizard).

Analytical Biochemistry (RUG, PIs: Peter Horvatovich and Rainer Bischoff)

• TAPP pipeline (Frank Suits, IBM Watson Center) for quantitative processing of single stage LC-MS data. Able to process data obtained with mass spectrometer of different resolution
  • grid: read mzdata.xml or mzxml data, mesh the raw to given resolution (other type of function are available too)
  • centroid: feature quantification tool, read the output of grid and provide the list of detected feature
  • Warp2D: time alignment of features list provided by the centroid module ref
  • metamatch: matching the same features across multiple feature list (chromatograms) resulting in a quantitative matrix of the matched features in different chromatograms

• msCompare (Berend Hoekman) is a framework interconnecting feature quantification and feature matching modules of different single stage quantitative data processing workflow. The included data rpocessing wrokflwos are the following:
  • MZmine feature quantification and feature matching module
  • OpenMS feature quantification and feature matching module
  • SuperHirn feature quantification and feature matching module
  • M-N rules feature quantification
  • inhouse matching module including Warp2D

• Time alignment algorithms using high quality preselected mass traces developed by Christin Christin (only Matlab script is currently available)
  • Correlation Optimized Warping using preselected mass traces with Component Detection Algorithm ref
  • Dynamic Time Warping using preselected mass traces with Component Detection Algorithm ref
  • Parametric Time using preselected mass traces with Component Detection Algorithm ref

Bioinformatics Laboratory (AMC, PIs: Antoine van Kampen, Perry Moerland, and Silvia Olabarriaga)

• Statistical data analysis pipeline for pre-processed quantitative MS data
  • readAPML: R script for converting an aligned APML file to (an external representation of) an ExpressionSet class for further analysis with R/Bioconductor.
  • QC: R script for quality control.
  • DE: R script for differential expression analysis.
  • CL: R script for classification.

Steps for adding tools to Netherlands Bioinformatics for Proteomics Platform (NBPP)

1. rename the template excel sheet (tool_workflow_template_final.xls) to your tool name. The excel sheet you can download from the root directory of the FTP server.
2. fill the excel sheet
3. login to the FTP server and make a directory with the tool name
4. upload the filled excel sheet, the tool, the example input and output files
5. add your tool to the list of Platform tool with explanation to NBIC Wiki: https://wiki.nbic.nl/index.php/Platform_tool

The FTP server is setup in a way that you can create a directory and place any files on it, but you can't delete them. If you need to delete files, then send email to Ishtiaq Ahmad (RUG) and/or Peter Horvatovich (RUG).