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Description, Instructions, and Tips for MS-Digest

Purpose

This document provides instructions for MS-Digest.

MS-Digest performs an in-silico enzymatic or chemical digest of one or more proteins and reports the mass of each predicted peptide. The proteins can either be accessed from a database by entering accession numbers or by entering user defined protein sequences.


Contents of this document:

Links to topics in the general instructions:

The MS-Digest output usually just lists singly charged peptides. If you check the Report Multiple Charges option the output will also include multiply charged peptides. The maximum number of charges a peptide can have is based on the number of basic amino acids in the peptide.


This parameter specifies the minimum m/z for fragments in the MS-Digest report. Set its value to zero if you want all fragments to be reported.


This parameter specifies the maximum m/z for fragments in the MS-Digest report.


This parameter specifies the minimum length for fragments in the MS-Digest report. At present it is a hidden parameter. Set its value to zero if you want all fragments to be reported.


These indicies are described in:

Bull, Henry B. and Breese, Keith (1974) "Surface Tension of Amino Acid Solutions: A Hydrophobicity Scale of the Amino Acid Residues", Arch. Biochem. Biophys, 161, 665-670


These indicies are described in:

Browne, C. A., Bennett, H. P. J. and Solomon, S. (1982) "The Isolation of Peptides by High-Performance Liquid Chromatography Using Predicted Elution Positions", Anal. Biochem., 124, 201-208