Average masses not matching up to online source
Reported by jtprince | May 14th, 2009 @ 11:48 AM
When I generate average masses for peptides using this:
require 'molecules'
Molecules::Libraries::Residue['C'].mass {|e|
e.std_atomic_weight.value }
=> 103.1429
The online resource here shows close (but significantly
different) average masses:
http://ca.expasy.org/tools/findmod/findmod_masses.html
They list cysteine at 103.1388
Comments and changes to this ticket
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bahuvrihi May 14th, 2009 @ 02:07 PM
My guess is that this is an issue of uncertainty and probably not a numerical issue. I'm fairly sure the numbers produced by the Molecules library are numerically correct, given the original data element data from NIST. No doubt the expasy numbers are numerically correct too, but they don't say where they got their numbers.
Given the uncertainty on the NIST data the numbers may be consistent. When you add the uncertainties directly (offhand I think that's the correct operation, but I haven't looked at this in a while):
Molecules::Libraries::Residue['C'].mass {|e| e.std_atomic_weight.uncertainty }.to_f # => 0.00825The correct value according to NIST is in [103.13465, 103.15115], which allows for 103.1429. This is definitely one of those quiet issues that is talked about too little. It's hard to figure out who is actually right. The physicist within me says that both are wrong unless you list uncertainty.
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jtprince May 14th, 2009 @ 03:23 PM
That sounds good. I was mostly worried I was doing the calculations wrong :)
Thanks!
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Mass Spectrometry Proteomics in Ruby
bahuvrihi
jtprince