Not sure how to do this for bioinformatics *Not sure what else is needed to calc

Question

Not sure how to do this for bioinformatics

*Not sure what else is needed to calculate the sequence and fragment, 2nd picture added

§ TOF/TOF

• TOF1 [collision cell] - TOF2

You use MS/MS methodology to fragment peptide ion #1 below using collision induced dissociation (CID): Peptide ion #1: LDNMAWVCK^2+ a. Sequence of the y_4 fragment ion? b. Name of the fragment ion LDNM^+? c. Peptide ion #1 could be generated from a complete trypsin digestion (i.e., no missed cleavages) of a protein. TRUE/FALSE

Explanation / Answer

y ions generates from the carboxyl terminus, or C-terminus.

Hence, for the given sequence,

y1 = K

y2 = KC

y3 = KCV

y4 = KCVW

Answer b. LDNM contains N-terminus and have four amino acids, the nomenclature will be b4.

Note: b ions generate from the N-terminus.

Answer c. The cleavage site to generate peptide #1 is between M and A which is not a trypsin cleavage site. Trypsin digestion occurs at either lysine or arginine amino acid.

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