Description, Instructions, and Tips for MS-Seq
Purpose
This document provides instructions for MS-Seq.
Contents of this document:
Links to topics in the general instructions:
- Search Times
- Stopping / Cancelling a Search
- Saving Hits from one Protein Prospector program, searching them with another
- Databases
- Species Filtering
- Intact Protein MW Filtering
- Enzyme specificity / Missed cleavages
- Frame Translation in DNA databases
- General features of links from program output
- Link from the accession number in program output to an annotated remote database entry
- Link from the MS-Digest index number in program output to MS-Digest
- Link from the peptide sequence in program output to MS-Product
- Constant Modifications
- User Specified Amino Acid
- Mass (m/z)
- Mass type
- Charge (z)
- Sample ID (comment)
- Max. Reported Hits
- AA Composition Ions
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.