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Average masses not matching up to online source

#15

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

Reported by jtprince · May 14th, 2009 @ 11:48 AM

State: new
Milestone: none
Assigned to: bahuvrihi bahuvrihi

Activity

  1. bahuvrihi
    bahuvrihi

    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
  # => 0.00825

    The 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.

    May 14th, 2009 @ 02:07 PM

  2. jtprince
    jtprince

    That sounds good. I was mostly worried I was doing the calculations wrong :)

    Thanks!

    May 14th, 2009 @ 03:23 PM

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