Tandem Mass Spectrometry Flashcards
What is the process of MS/MS
Ionisation->Separation->Dissociation in collision cell-> separation->Ion Detection
What is the difference in use of the quadrupole between MS/MS and MS
In MS the quadrupole is used only as a guide, in MS/MS it used to separate ions, and TOF used for analysis
At how many different bonds can the carbon backbone fragment in a peptide?
3 different bonds: NH-CH, CO-NH and CH=CO
What is the most common bond to break? What fragments does this produce?
CO-NH bond is most commonly broken, produces bn and yn-2 fragments
What is the Immonium ion?
The smallest residue fragment consisting of only one residue
Which side is charge retained for a, b and c ions?
Charge is retained on amine side (Low letters=left)
Which side is charge retained for x, y, and z fragments?
Charge is retained on the carboXYlZ side
Does a more or less charged species provide more informative spectra?
Highly charged species provide a more useful spectra
How do we calculate the overall charge on a peptide fragment?
Calculate the number of Arginine (R), Lysine (K) and Histidine (H) species + N-terminus amine charge + C-terminus if amide
What does the signal intensity of a spectra reflect?
Signal intensity = peak height, showing how often bond breaks
How would we calculate the mass of a residue from its AA mass?
AA mass - 18Da (mass of H2O)
What is the letter code used for the presence of either L or I (Leu/Ile)?
X
How do you calculate the mass of a bn ion?
bn mass = Sum of residue masses + 1Da
How do you calculate the mass of an an ion?
bn - 28Da
What is MH+?
MH+ is the total residue mass of the protein
