Description, Instructions, and Tips for MS-Product

Purpose
This document provides instructions for MS-Product.

Instructions for ProteinProspector Programs

Contents of this document:

Links to topics in the general instructions:

Instrument Specific Ion Types

MS-Product can either display the ion types specific to the selected instrument or those which are selected by using the available check boxes on the input form.

Fragment-Ion types

Check the boxes next to each ion type to list the corresponding fragment ion masses in the MS-Product output. The default ion-types are those generally seen in MALDI Post-Source Decay (PSD) spectra. The default water loss amino acids are S and T. The default ammonia loss amino acids are R, K and Q. The default positive charge bearing amino acids are R, H and K.

Currently supported ion types include:

Ion typeRestrictions
a, b, x, y, Y no restrictions
c not if C terminal residue of the fragment is P
z not if N terminal residue of the fragment is P
a-NH3, b-NH3, y-NH3 ion contains ammonia loss amino acid
b-H2O ion contains water loss amino acid
b+H2O ion contains positive charge bearing amino acid; only bn-1, bn-2 ( length n)
a-H3PO4, b-H3PO4, y-H3PO4 ion contains phosphorylated S,T or Y
b-SOCH4, y-SOCH4 ion contains oxidized M
internal b no restrictions
internal a no restrictions
internal b-H2O ion contains water loss amino acid
internal b-NH3 ion contains ammonia loss amino acid
N-term ladder removal of N term residues (y equiv.)
C-term ladder removal of C term residues (b+H2O equiv.)
da, db not if C terminal residue of the ion is F, W or Y, substituent must be defined in aa.txt
v no restrictions
wa, wb not if N terminal residue of the ion is F, W or Y, substituent must be defined in aa.txt

Max. Reported Charge

MS-Product can calculate the m/z values of multiply charged fragment ions. The maximum charge for a given fragment depends on the number of basic amino acids in it. The Max Reported Charge item allows you set a limit on the maximum charge displayed. Which amino acids are considered basic depends on the Instrument you have selected.