wiki:FeatureDetection

Feature Detection

Introduction

Proteios SE supports feature detection using external program packages msInspect and OpenMS. Two OpenMS programs are supported, PeakPicker and FeatureFinder. Output from feature detection from msInspect is a tab-separated value (tsv) file, while OpenMS program FeatureFinder produces an XML file.

How to Perform Feature Detection using msInspect

Currently feature detection for mzML and mzXML peaklist files are supported.

  1. Select File -> Select project -> (List of projects) and select the project of interest.
  2. Select <Active Project> -> Files. Navigate to the directory with files to use.
  3. Click the check boxes for peaklist files to be used.
  4. Select Extensions -> Use spectrum file(s) for msInspect feature detection.
  5. Select strategy if you don't want to use the default one.
  6. Click Next - Create feature detection job[s].
  7. One feature detection job will now be created for each selected peaklist file. Wait for the job(s) to finish.
  8. The generated feature detection file for a peaklist file can be found in the project directory. The filename consists of the filename of the peaklist file (including file extension) and added file extension ".peptides.tsv".

How to Perform Feature Detection using OpenMS

Currently feature detection for mzML files are supported. The two supported OpenMS programs PeakPicker and FeatureFinder can be processed in a pipeline, where PeakPicker processes an input mzML file and produces a new one with selected peaks, which are used as input to FeatureFinder, that produces a resulting *.featureXML features file.

The produced results will be uploaded to a file with name constructed as follows:

  1. Base filename of the peaklist file (filename without file extension)
  2. + ".peakpicker.mzML" or ".featurefinder.featureXML"

The file extension used depends on the used OpenMS program. If the programs are used in a pipeline, the PeakPicker result file is only uploaded if specifically requested, and file extension ".peakpicker.featurefinder.featureXML" is used for the final FeatureFinder result file.

  1. Select File -> Select project -> (List of projects) and select the project of interest.
  2. Select <Active Project> -> Files. Navigate to the directory with files to use.
  3. Click the check boxes for peaklist files to be used.
  4. Select Extensions -> Use spectrum file(s) for OpenMS feature detection.
  5. Select OpenMS program as one of:
    a. PeakPicker + FeatureFinder
    b. PeakPicker
    c. FeatureFinder
  6. Select "High resolution" or "Wavelet" PeakPicker algorithm.
  7. Select "Centroided" or "Isotope wavelet" FeatureFinder algorithm.
  8. Click check box if PeakPicker result file should be uploaded when working in pipeline.
  9. Click Next - Create feature detection job[s].
  10. One or two (if "PeakPicker + FeatureFinder" was selected) feature detection jobs will now be created for each selected peaklist file. Wait for the job(s) to finish.
  11. The generated feature detection file for a peaklist file can be found in the project directory. The filename consists of the base filename of the peaklist file (filename without file extension) and file extension ".featurefinder.featureXML" or ".peakpicker.featurefinder.featureXML" (if "PeakPicker + FeatureFinder" was selected).
  1. Label-free quantitative analysis
Last modified 11 years ago Last modified on Mar 25, 2011, 11:10:33 AM