Question 1

My program predicts 74 fragments for protein 4
and the observed data shows 72 fragments, so it is 
likely to be protein 4.  By sorting the predicted
masses and comparing them to what was observed, it 
looks most of them match up correctly.  However,
there are several differences.  

There is one example of incomplete tryptic digestion.
For example, we predict two extra R fragments that aren't
observed.  Each R weighs 174.2, and in the observed 
masses there is one at 348.4 that we didn't predict - so
this represents the RR that was not cut by trypsin.  

Two other fragments that we predict (LPFPK and LSFSR) also
appear together in the observed masses.  However, these
two fragments are not next to eachother in the primary 
protein sequence, so they might have been covalently attached
in the protein.

There also appear to be two cases where an amino acid has
been phosphorylated which causes a different weight to be
observed.  TLAR (459.59) appears as 538.59 which is 79 Da
higher - the weight of a phosphate group added to threonine.
Similar case with LSAFDAHFAGR which appears as the 1270.45
fragment (79 above the expected 1191.45).  In this case the 
serine would be phosphorylated.

Question 2

Given that it was assumed a charge state of 2, the two mos abundant peaks will
be for the 0C13 isotope and the 1C13 isotope, the weights will be 727.97/2 and
728.97/2.


Since all fragments in MS2 have a charge of 1, the following are the two peaks for each daughter ion - 
if you use the amino acid weights minus water, you just add
1 to the B ions and 19 to the Y ions.

		B ions		Y ions
S		88.09		641.88	CHLLR	
SC		191.25		538.72	HLLR
SCH		328.41		401.56 	LLR
SCHL		441.59		288.38	LR
SCHLL		554.77		175.2	R