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Finding Protein Sequences Using PROWL

Ronald Beavis¹, David Fenyö²

¹Beavis Informatics Ltd., Winnipeg, Manitoba, Canada
²GE 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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Unit Introduction
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: 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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Figures

Figure 13.2.1

The start page for a PepFrag session.

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Figure 13.2.2

Results obtained from a PepFrag search.

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Figure 13.2.3

The start page for a GPM session.

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Figure 13.2.4

Initial results page obtained from a GPM search.

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Figure 13.2.5

Homologue page for one protein.

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Figure 13.2.6

Protein model page, upper section showing sequence coverage.

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Figure 13.2.7

Protein model page, lower section showing spectrum assignments.

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Figure 13.2.8

The peptide model display page.

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Figure 13.2.9

The start page for a ProFound session.

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Figure 13.2.10

Results obtained from a ProFound search.

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Figure 13.2.11

Details of a match between the data and a protein sequence.

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Literature Cited

Literature Cited
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