Calculating Protein Mass

06 Jul 2024 in Study / Rosalind on Rosalind problem

A problem from rosalind “Bioinformatics Stronghold” category, Dictionary

• A problem from rosalind “Bioinformatics Stronghold” category
  Rosalind Problem Link

• Description

  • Mass Spectrometry
    • “an analytical chemical technique used to determine the mass, elemental composition, and structure of molecules”
    • Monoisotopic Mass
      • There are various isotopic substance (Even if they are same substance, their mass is different from each other)
      • If we calculate total mass through monoisotopic mass, we need to use the most abundant isotope’s mass
    • Average Mass
      • If we calculate total mass through average mass, we need to use the average mass of atoms
  • Protein Mass = Mass(residue 1) + Mass(residue 2) + … + Mass(residue n) - (n - 1) x Mass(H₂O)
    • Because of Dehydration reaction
    • In several experiment, we often ignore non-residue’s mass (water) when we calculate the protein mass
      • This is a safe assumption because we often do Tandem Mass Spectrometry
      • Tandem Mass Spectrometry: “protein is first divided into peptides, which are then broken into ions for mass analysis”
  • There is a Monoisotopic Mass Table for each amino acid

My Solution

• Code

mass_table = {"A" : 71.03711, "C" : 103.00919, "D" : 115.02694, "E"  : 129.04259, "F"  : 147.06841, "G"  : 57.02146, "H"  : 137.05891, "I"  : 113.08406, "K"  : 128.09496, "L"  : 113.08406, "M"  : 131.04049, "N"  : 114.04293, "P"  : 97.05276, "Q"  : 128.05858, "R"  : 156.10111, "S"  : 87.03203, "T"  : 101.04768, "V"  : 99.06841, "W"  : 186.07931, "Y"  : 163.06333}

name = input()
f = open(name, 'r')
aaSeq = ""

for line in f.readlines():
    aaSeq += line[:-1]


mass = 0

for i in range(len(aaSeq)):
    mass += mass_table[aaSeq[i]]

print(mass)
f.close()