Finding Protein Sequences Using PROWL

Ronald Beavis1, David Fenyö2

1 Beavis Informatics Ltd., Winnipeg, Manitoba, 2 GE Healthcare, Piscataway, New Jersey
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.2
DOI:  10.1002/0471250953.bi1302s7
Online Posting Date:  October, 2004
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Abstract

PROWL is a collection of tools for the identification of protein sequences, using input data derived from mass spectrometry. Experimental data from various types of mass spectrometers can be input directly into PROWL's component software. This unit presents protocols for several of the individual PROWL tools. Specifically, PepFrag allows for the analysis of a single spectrum derived from tandem mass spectrometry. GPM, on the other hand, provides for the analysis of multiple MS/MS spectra. An additional protocol introduces ProFound for analyzing a single spectrum of peptide mass fingerprinting data.

     
 
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Table of Contents

  • Basic Protocol 1: Using PROWL with the Web Interface from the Rockefeller Server with Tandem Mass Spectrometry (MS/MS) Data: PepFrag
  • Basic Protocol 2: Using PROWL with the Web Interface from the Rockefeller Server with Tandem Mass Spectrometry (MS/MS) Data: GPM
  • Support Protocol 1: Using Advanced Features for GPM Searches
  • Basic Protocol 3: Using PROWL with the Web Interface from the Rockefeller Server with Peptide Fingerprinting Mass Spectrometry (MS) Data: ProFound
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

Literature Cited
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