4 ms·

However for proteins - which, even if broken down to small peptides in the mass spec, have large numbers of C, N, O, H atoms then monoisotopic makes no sense.

eesmith 7y ago
https://patents.google.com/patent/US20050267689A1/en https://patents.google.com/patent/US20050267689A1/en disagrees with you, saying: > Leftmost peaks in isotopic clusters correspond to molecules containing only the lowest-mass isotopes of all their atoms: all carbon atoms are C-12, all hydrogen atoms are H-1, all nitrogen atoms are N-14, and so on. These peaks are known to those skilled in the art as monoisotopic peaks. While each chemical species of molecule manifests itself in the mass spectrum as an isotopic cluster, it is characterized by only one monoisotopic peak, thus it became common practice to characterize molecules in the mass range of up to approximately 10 kDa by their monoisotopic masses. For example, it became common practice to use monoisotopic masses in protein identification methods based on comparing mass spectral data to databases of masses of protein fragments. https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/monoisotopic-mass https://www.sciencedirect.com/topics/biochemistry-genetics-a... also disagrees, quoting from "Protein Identification by Peptide Mass Fingerprinting (PMF)", Nachimuthu Saraswathy, Ponnusamy Ramalingam, in Concepts and Techniques in Genomics and Proteomics, 2011 > 13.4 Data analysis and identification of protein > The peak list is compared with a peak list generated from the database proteins. The commonly used computer search engines are MS-Fit, Mascot, Peptident, Profound, etc. The monoisotopic mass of the each peak, the protease used, the number of missed cleavages in order to account for the possible incomplete digestion are given as input. That is, it appears that monoisotopic mass makes good sense for small peptides in mass spectroscopy.
- DrScientist 7y ago
  Let's take a short tryptic peptide. LQGIVSWGSGCAQK Formula is C62 N18 O19 S1 H100 Let's look at C - C12 is around 98.93 natural abundance, the N 99.6, O 99.76, H 99.98 If we forget the others for simplicity of calculation and only look at C. Then the probability of getting a peptide with all C12 is 0.9893^62 ~ 0.51 ie only half of the sample will be monoisotopic mass - double the length of the peptide and it's down to a quarter - full length protein you are looking at vanishingly small amounts. The original problem was to calculate masses of things upto 1000aa - something of 1000aa would have a frequency of monoisotopic species of 2.04058E-21 - ie a handful of molecules out of 6x10^23 of a mole. The value of monoisotopic values decreases as the size and complexity of the molecule goes up.
  - eesmith 7y ago
    You wrote: "The value of monoisotopic values decreases as the size and complexity of the molecule goes up." Yes, that is is agreement with the text I quoted earlier - "it became common practice to characterize molecules in the mass range of up to approximately 10 kDa by their monoisotopic masses". Note (from another part of the second link I gave) "This eight amino acid peptide was named GmPep914 (DHPRGGNY), based on its monoisotopic mass." So, there's plenty of clear evidence that people do use monoisotopic masses for mass spectra analysis of at least some peptides. What is your point? That this question is poorly written? I think I started this thread to point that out.
    - DrScientist 7y ago
      My point was that while for small molecules, the mono-isotopic mass makes perfect sense as it's the major species, for larger proteins it isn't and indeed becomes a vanishingly small proportion. Note for something around 10kda the difference between the average and mono-isotopic mass will be around ~6 daltons - with the experimental accuracy around ~1 dalton!
      - eesmith 7y ago
        You write now that it makes perfect sense. However, at https://news.ycombinator.com/item?id=22383816 https://news.ycombinator.com/item?id=22383816 you wrote "even if broken down to small peptides in the mass spec, ... then monoisotopic makes no sense". It was that latter point that I contested, because the literature clearly indicates that for at least some small peptides it makes sense.
        DrScientist 7y ago
        Depends on your definition of small - but I accept the point that if the peptides are small enough it can be useful and I went too far there. Remember the problem posed was to calculate the mass of proteins upto 1000aa where the difference between mono-isotopic mass and real average mass would be many 10's of daltons - much more than the missing water!

eesmith 7y ago

https://patents.google.com/patent/US20050267689A1/en https://patents.google.com/patent/US20050267689A1/en disagrees with you, saying: > Leftmost peaks in isotopic clusters correspond to molecules containing only the lowest-mass isotopes of all their atoms: all carbon atoms are C-12, all hydrogen atoms are H-1, all nitrogen atoms are N-14, and so on. These peaks are known to those skilled in the art as monoisotopic peaks. While each chemical species of molecule manifests itself in the mass spectrum as an isotopic cluster, it is characterized by only one monoisotopic peak, thus it became common practice to characterize molecules in the mass range of up to approximately 10 kDa by their monoisotopic masses. For example, it became common practice to use monoisotopic masses in protein identification methods based on comparing mass spectral data to databases of masses of protein fragments. https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/monoisotopic-mass https://www.sciencedirect.com/topics/biochemistry-genetics-a... also disagrees, quoting from "Protein Identification by Peptide Mass Fingerprinting (PMF)", Nachimuthu Saraswathy, Ponnusamy Ramalingam, in Concepts and Techniques in Genomics and Proteomics, 2011 > 13.4 Data analysis and identification of protein > The peak list is compared with a peak list generated from the database proteins. The commonly used computer search engines are MS-Fit, Mascot, Peptident, Profound, etc. The monoisotopic mass of the each peak, the protease used, the number of missed cleavages in order to account for the possible incomplete digestion are given as input. That is, it appears that monoisotopic mass makes good sense for small peptides in mass spectroscopy.

DrScientist 7y ago
Let's take a short tryptic peptide. LQGIVSWGSGCAQK Formula is C62 N18 O19 S1 H100 Let's look at C - C12 is around 98.93 natural abundance, the N 99.6, O 99.76, H 99.98 If we forget the others for simplicity of calculation and only look at C. Then the probability of getting a peptide with all C12 is 0.9893^62 ~ 0.51 ie only half of the sample will be monoisotopic mass - double the length of the peptide and it's down to a quarter - full length protein you are looking at vanishingly small amounts. The original problem was to calculate masses of things upto 1000aa - something of 1000aa would have a frequency of monoisotopic species of 2.04058E-21 - ie a handful of molecules out of 6x10^23 of a mole. The value of monoisotopic values decreases as the size and complexity of the molecule goes up.
- eesmith 7y ago
  You wrote: "The value of monoisotopic values decreases as the size and complexity of the molecule goes up." Yes, that is is agreement with the text I quoted earlier - "it became common practice to characterize molecules in the mass range of up to approximately 10 kDa by their monoisotopic masses". Note (from another part of the second link I gave) "This eight amino acid peptide was named GmPep914 (DHPRGGNY), based on its monoisotopic mass." So, there's plenty of clear evidence that people do use monoisotopic masses for mass spectra analysis of at least some peptides. What is your point? That this question is poorly written? I think I started this thread to point that out.
  - DrScientist 7y ago
    My point was that while for small molecules, the mono-isotopic mass makes perfect sense as it's the major species, for larger proteins it isn't and indeed becomes a vanishingly small proportion. Note for something around 10kda the difference between the average and mono-isotopic mass will be around ~6 daltons - with the experimental accuracy around ~1 dalton!
    - eesmith 7y ago
      You write now that it makes perfect sense. However, at https://news.ycombinator.com/item?id=22383816 https://news.ycombinator.com/item?id=22383816 you wrote "even if broken down to small peptides in the mass spec, ... then monoisotopic makes no sense". It was that latter point that I contested, because the literature clearly indicates that for at least some small peptides it makes sense.
      - DrScientist 7y ago
        Depends on your definition of small - but I accept the point that if the peptides are small enough it can be useful and I went too far there. Remember the problem posed was to calculate the mass of proteins upto 1000aa where the difference between mono-isotopic mass and real average mass would be many 10's of daltons - much more than the missing water!