Description, Instructions, and Tips for MS-Seq


This document provides instructions for MS-Seq.

Contents of this document:

Links to topics in the general instructions:

Introduction and Background

MS-Seq is our implementation of the algorithm described in Mann, M. and Wilm, M. Anal. Chem. 1994, 66, 4390-4399. In addition to the algorithm described in the paper our implementation has the features listed below.

  • Spectra need not be pre-interpreted to a peptide sequence tag. The data is simply entered as the mass/charge and charge as measured by a mass spectrometer.
  • Whilst the data must belong to a single ion series of a, b, c or y ions ( allows all series simultaneously) any number of peaks from the same ion series may be entered in MS-Seq and the gap between any of the peaks may be greater than a single amino acid.
  • MS-Seq is a fully featured Protein Prospector program with all the standard options such as molecular weight and species pre-searches, multiple digest options, etc.
  • Searches can be restricted to matching sequences which include/exclude particular amino acids or a regular expression of amino acids.