Opened 2 years ago

Last modified 2 years ago

#1095 assigned defect

Sulfation support: ticket 1 - correct mass of neutral loss

Reported by: dbrentw Owned by: dbrentw
Priority: normal Milestone: GRITS - 1.2 SR3
Component: MS annotation management Version: GRITS 1.2.x
Severity: major Keywords:
Cc:

Description

When Glycoworkbench fragments a sulfated glycan, one of the fragments will be the intact structure w/out the sulfate. This neutral loss mass is not calculated properly, as it is 18da too heavy (water). Whenever there is a neutral loss of sulfate, we need to subtract 18da from the fragment molecular mass.

Change History (1)

comment:1 Changed 2 years ago by Rene Ranzinger

There are actually multiple fragments that can generated a glycan portion with the loss of the sulfate.

This is a gws sequence with a 6Sulfate:
b1D-GlcNAc,p/#bcleavage--3b1D-Gal,p--6?1S$MONO,Und,0,0,freeEnd

This is how it looks when the sulfate is cleaved of:
b1D-GlcNAc,p/#bcleavage--3b1D-Gal,p--6?1S/#lcleavage$MONO,Und,0,0,freeEnd

So the key sequence for neutral loss of S would be S/#lcleavage. Any appearance of this sequence should result in a -18.

Note: See TracTickets for help on using tickets.