Finding protein sequences using PROWL

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.