Description, Instructions, and Tips for MS-Seq

Instructions for ProteinProspector Programs

Contents of this document:

• Introduction and Background

• Search Times
• Stopping / Cancelling a Search
• Saving Hits from one ProteinProspector 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
• Modified N or C Terminal Groups
• Modified Cysteine Residues
• User Specified Amino Acid
• Mass (m/z)
• Mass type
• Charge (z)
• Sample ID (comment)
• Max. Reported Hits
• AA Composition Ions

Introduction and Background

• 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 ProteinProspector 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.