applications of MS

Question 1

Structure elucidation - small changes

Answer 1

can be used to determine small differences/changes in molecular structure
Spectra from related compounds - list peaks common to both and which are unique. common peaks can’t contain site of methylation, can produce fragmentation mechanisms for the common peaks and unique peaks

Question 2

Structure elucidation - isomers

Answer 2

can be used to separate isomers.
using fragmentation studies by CI-MS/MS or ESI- MS/MS, it is possible to isolate key structural alterations and linkage isomerism
Interested in peaks that are different which you can create a mechanisms for an identify which isomer relates to which spectra

Question 3

Proteomics

Answer 3

the study of protein structure and function

a range of analytical techniques

Question 4

Proteomics - protein mass determination

Answer 4

first need to be able to measure the molecular weight of the protein
deconvolute a multiply charged envelope of molecular ions and calculate the molecular weight of a protein

Question 5

Proteomics - experimental

Answer 5

Perform an ESI MS analysis of protein analyte
assign charges to observed peaks
calculate molecular weight

Question 6

Protein mass determination - equations

Answer 6

Multiply charged molecular ions of the type [M+nH]n+
m1= (M+n1)/n1 
m2 = (M+n2)/n2
where M = molecular weight of protein 
n= number of charges 
mn= observed m/z in ESI-MS 
m2

Question 7

Peptide sequencing

Answer 7

finding the amino acid sequence of a peptide by ESI-MS/MS. Peptides are formed by condensation polymerisation of amino acids
Peptide fragment in MS/MS by cleavage a (or next to) the peptide bond. fragment ions are formed by cleavage of the peptide bond with the charge being retained by C-terminus are called y-ions. Y-ions will be formed by cleavage of all peptides in the chain simultaneously (not sequential)
y-ions differ by one amino acid, residue masses of amino acids are 18 Da less than the amino-acid weight.

Question 8

Peptide sequencing methodology

Answer 8

1. analyse sample with peptide of interest. obtain MS in quadrupole 1
2. isolate precursor ion for peptide
3. send precursor ion into collision cell. fragment precursor ions
4. measure product ion spectrum. peptide has fragmented to produce 6 product ions
   differences in m/z between neighbouring y-ions correspond to the amino acid residue mass. ion y1 has no peptide bond and is charged and so is 19 Da higher than the corresponding residue mass (18 for water, 1 for charge)