[Biopython-dev] Updates to protein weights

Yeager, Mark D mark_yeager at merck.com
Wed Aug 6 09:46:57 EDT 2003

I am very new to Python and Biopython, so I may be making some irrelevant

For those doing mass spectroscopy (proteomics), it might be beneficial to
include monoisotopic as well as average MW for the amino acids, and
bookkeeping of the additional H2O for a polypeptide could be done at the end
of the calculation.

For example here are a couple amino acids without H2O

 	Monoiso.	Average	
A	71.03711	71.0788	
R	156.10111	156.1875	
monoiso H2O= 18.01057
average H2O= 18.0152

(I'm not sure about the accuracy of average H20 -- have to dig into IUPAC)

With the spreading use of highly accurate FTICR (Fourier transform ion
cyclotron resonance) mass spec, this might be a good thing to have in place
sooner rather than later.

Carbon is a mix of 12C and 13C isotopes (and 14C which we neglect here).
Natural abundance of 98.9% and 1.1%.
By definition 12C = 12.00000 and all other isotope masses refer to this
13C = 13.00335.1 
1H = 1.00783
16O is 15.99491.


-----Original Message-----
From: Yair Benita [mailto:Y.Benita at pharm.uu.nl]
Sent: Wednesday, August 06, 2003 2:34 AM
To: biopython-dev at biopython.org
Subject: [Biopython-dev] Updates to protein weights

The protein weights in Bio-> Data -> IUPACData are not accurate enough. For
large proteins I get an error which is unacceptable. Can someone with access
please update them:

protein_weights = {
    "A": 89.09,
    "C": 121.16,
    "D": 133.10,
    "E": 147.13,
    "F": 165.19,
    "G": 75.07,
    "H": 155.16,
    "I": 131.18,
    "K": 146.19,
    "L": 131.18,
    "M": 149.21,
    "N": 132.12,
    "P": 115.13,
    "Q": 146.15,
    "R": 174.20,
    "S": 105.09,
    "T": 119.12,
    "V": 117.15,
    "W": 204.23,
    "Y": 181.19}

Yair Benita
Pharmaceutical Proteomics
Faculty of Pharmacy
Utrecht University

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