5 ms·

As an aside - monoisotopic mass is a strange one to use. In the real world you are a mixture of isotopes, so it's better to use the average mass ( average of t

As an aside - monoisotopic mass is a strange one to use. In the real world you are a mixture of isotopes, so it's better to use the average mass ( average of the different isotope masses, corrected for abundance ) if you want to compare to experimentally determined masses - say from mass spec. It's not as if average mass is more complex - for the sake of these calculations it's still just a number looked up from a table... ie why oh why use the wrong value when it's just as easy to use the right one ()? () true it's biology so there isn't a right one in all circumstances - lots of interesting effects eg enzymes having slightly different rates of incorporation for different isotopes - however it's closer to the truth than mono-isotopic.

eesmith 7y ago
https://en.wikipedia.org/wiki/Monoisotopic_mass#Monoisotopic_mass_in_spectrometry https://en.wikipedia.org/wiki/Monoisotopic_mass#Monoisotopic... points out: > The monoisotopic mass is not used frequently in fields outside of mass spectrometry because other fields cannot distinguish molecules of different isotopic composition. For this reason, mostly the average molecular mass or even more commonly the molar mass is used. For most purposes such as weighing out bulk chemicals only the molar mass is relevant since what one is weighing is a statistical distribution of varying isotopic compositions. > This concept is most helpful in mass spectrometry because individual molecules (or atoms, as in ICP-MS) are measured, and not their statistical average as a whole. Since mass spectrometry is often used for quantifying trace-level compounds, maximizing the sensitivity of the analysis is usually desired. By choosing to look for the most abundant isotopic version of a molecule, the analysis is likely to be most sensitive, which enables even smaller amounts of the target compounds to be quantified. Therefore, the concept is very useful to analysts looking for trace-level residues of organic molecules, such as pesticide residue in foods and agricultural products.
- DrScientist 7y ago
  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

https://en.wikipedia.org/wiki/Monoisotopic_mass#Monoisotopic_mass_in_spectrometry https://en.wikipedia.org/wiki/Monoisotopic_mass#Monoisotopic... points out: > The monoisotopic mass is not used frequently in fields outside of mass spectrometry because other fields cannot distinguish molecules of different isotopic composition. For this reason, mostly the average molecular mass or even more commonly the molar mass is used. For most purposes such as weighing out bulk chemicals only the molar mass is relevant since what one is weighing is a statistical distribution of varying isotopic compositions. > This concept is most helpful in mass spectrometry because individual molecules (or atoms, as in ICP-MS) are measured, and not their statistical average as a whole. Since mass spectrometry is often used for quantifying trace-level compounds, maximizing the sensitivity of the analysis is usually desired. By choosing to look for the most abundant isotopic version of a molecule, the analysis is likely to be most sensitive, which enables even smaller amounts of the target compounds to be quantified. Therefore, the concept is very useful to analysts looking for trace-level residues of organic molecules, such as pesticide residue in foods and agricultural products.

DrScientist 7y ago
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.