Using ProSight PTM and Related Tools for Targeted Protein Identification and Characterization with High Mass Accuracy Tandem MS Data

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Abstract
ProSight PTM v2.0, neuroProSight, and the Sequence Gazer allow the identification and characterization of proteins from high mass accuracy tandem mass spectrometric data of intact proteins and large peptides. Input data consists of one or more neutral precursor ion masses and a set of neutral b/y or c/z. fragment ions masses. This data is compared against “shotgun annotated” proteome databases or known protein sequences. With these tools it is possible to not only identify unknown proteins, but to determine the location of post‐translational modifications (PTM) with 100% sequence coverage. Collectively, the tools create a search environment that allows five different search modes, including absolute mass and sequence tag searching, which are conveniently employed via a graphical user interface. Data management and chemical noise reduction tools are also available. These tools provide a complete environment for the identification and characterization of proteins from high resolution tandem mass spectrometry of intact proteins and large peptides. Curr. Protoc. Bioinform. 19:13.6.1‐13.6.28. © 2007 by John Wiley & Sons, Inc.