CSE 190: Assignment 3
Due Feb 25th, 2022
Late Due Date Mar 1st, 2022 for 50% credit
(15 points)
Complete the following questions and upload a PDF of your answers to Gradescope. Please be sure to
describe your approach thoroughly and partial credit may be awarded even if the final answer is incorrect.
Questions
1. Given the following spectrum of sequence mass 15 in a species with only two amino acids,
mass(A) = 2 Da and mass (B) = 3 Da, calculate the number of possible sequences matching five
peaks to the spectrum. Attach a printout of the completed spreadsheet. (4 points)
2. Using the following mappings between peptides and proteins, where each protein might be from a
different species.
a. Which, if any, proteins are matched by peptides that don’t match to any other protein? (1
point)
b. Which proteins are subset proteins (match to a subset of peptides of another protein)?
What is a potential explanation for a protein matching a subset of peptides also matched
by another protein? (2 points)
c. Applying the maximum parsimony algorithm from slide 19 in the slide deck for lecture 12,
what would be the resulting set of parsimonious proteins identifications?How many
species are in the output? (3 points)
3. Using the following table of peptides mapping to proteins from the SARS-CoV-2 data
Peptide sequence Proteins
ASNPFLPGGGPATGPSVTNPFQPAPPATLTLNQLR
sp|Q9Y6I3-3|EPN1_HUMAN
sp|Q9Y6I3|EPN1_HUMAN
sp|Q9Y6I3-1|EPN1_HUMAN
PSTNGTTAGGFDTEPDEFSDFDRLR
sp|Q9Y6I3-3|EPN1_HUMAN
tr|K7EMP4|K7EMP4_HUMAN
PSTNGTTAAGGFDTEPDEFSDFDR
sp|Q9Y6I3-1|EPN1_HUMAN
tr|K7EMP4|K7EMP4_HUMAN
EEADQPPSCGPEDDAQLQLALSLSR sp|Q9Y6I3|EPN1_HUMAN
NIVHNYSEAEIK
sp|Q9H201-2|EPN3_HUMAN
sp|Q9Y6I3-3|EPN1_HUMAN
sp|Q9Y6I3|EPN1_HUMAN
sp|Q9Y6I3-1|EPN1_HUMAN
SPGAFDMSGVR
sp|Q9Y6I3-3|EPN1_HUMAN
sp|Q9Y6I3|EPN1_HUMAN
sp|Q9Y6I3-1|EPN1_HUMAN
ENMYAVQTLK
sp|Q9Y6I3-3|EPN1_HUMAN
sp|Q9Y6I3|EPN1_HUMAN
sp|Q9Y6I3-1|EPN1_HUMAN
LQMAIEESKR
sp|Q9Y6I3-1|EPN1_HUMAN
sp|Q9Y6I3|EPN1_HUMAN
sp|Q9Y6I3-3|EPN1_HUMAN
LQMAIEESK
sp|Q9Y6I3-1|EPN1_HUMAN
sp|Q9Y6I3|EPN1_HUMAN
sp|Q9Y6I3-3|EPN1_HUMAN
.
a. Which proteins (if any) are subsumable? For each subsumable protein, also indicate
which other protein(s) make it subsumable. (2 points)
b. Applying the maximum parsimony algorithm from slide 19 in the slide deck for lecture 12,
what would be the resulting set of parsimonious proteins identifications? (3 points)