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.
- Report Multiple Charges
- Minimum Fragment Mass
- Maximum Fragment Mass
- Minimum Fragment Length
- Bull Breese Indicies
- HPLC Indicies
- Databases
- Digestion of a User Supplied Sequence
- Frame Translation in DNA databases
- Output
- Saving Hits from one Protein Prospector program, searching them with another
- Database Entry Retrieval Method
- List of Entries
- Enzyme specificity / Missed cleavages
- End Terminus
- General features of links from program output
- Hide HTML Links
- Link from the peptide sequence in program output to MS-Product
- Constant Modifications
- Variable Modifications
- User Specified Amino Acid
- Hide Protein Sequence
- Present Amino Acids
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