Description, Instructions, and Tips for MS-Digest

Purpose
This document provides instructions for MS-Digest.

Instructions for ProteinProspector Programs

Contents of this document:

Links to topics in the general instructions:

Hide Protein Sequence

The complete protein sequence is normally displayed in the MS-Digest output. You can disable this display using the Hide Protein Sequence option.

Report Multiple Charges

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.

Hide HTML Links

The outputs from ProteinProspector programs usually contains links to other ProteinProspector programs and Internet pages (general features of links from program output). You can disable these links by checking the Hide HTML Links option. This will have the effect of considerably reducing the size of the output report and hence the network traffic.

Digestion of a User Supplied Sequence

To use MS-Digest to digest a user supplied sequence:

1). select User Protein as the Database option;

2). paste or type the sequence in the Protein Sequence box having first deleted the instructions;

    Tabs, returns, and spaces are ignored.

    USE CAPITAL LETTERS. The following lower case letters can be used:
    s,t,y - Phosphorylated S,T,Y
    u - user specified amino acid
    Do NOT use the letters B, J, O, U, X, or Z.

    Do NOT use 3-letter code amino acid symbols.

3). set the other MS-Digest parameters as appropriate;

4). press the Perform Digest button.

Database Entry Retrieval Method

It is possible to retrieve entries from the database by specifying either the Accession Number or the Index Number. The accession number is a unique identifier for a protein within the database. It will not change between subsequent revisions of the database and is external to the ProteinProspector package. The index number for a particular protein is internal to the ProteinProspector package and is likely to change when you update the database. Both the index number and the accession number are reported in ProteinProspector search results. Entries are generally more efficiently retrieved using index numbers.

Minimum Fragment Mass

This parameter specifies the minimum m/z 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.

Minimum Fragment Length

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.

End Terminus

The End Terminus parameter selects end terminal processing of the digest fragments. The stripping terminus parameter is used to specify which terminus the amino acids are stripped from. The stripping range specifies the range of the number of amino acids which are cleaved off.