4 ms·

This site was developed by Pavel Pevzner, who teaches bioinformatics at UCSD. We used this site as the main curriculum in one of our final bioinformatics class,

This site was developed by Pavel Pevzner, who teaches bioinformatics at UCSD. We used this site as the main curriculum in one of our final bioinformatics class, and after solving ~ 10 - 15 problems a week for 10 weeks, I don't recall a single time where the error was in the problem set solutions. Re: the problem - not a hundred percent on this, but I think the issue is that they are vague on the fact that this is a theoretical question, not a practical one. The key is that the question itself does not mention the addition of the water molecule, just that you have a sequence P with a dictionary of weights. Edit 1: If memory serves me correct, after the initial ionization phase of mass spectroscopy, the additional water molecule is discarded, making it insignificant in the analysis of your peptide sequences. Edit 2: If anyone is interested in following through this site, I would highly recommended using the existing problem tracks http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track http://rosalind.info/problems/list-view/?location=bioinforma... These will help lay out the problems in a logical order an ensure you have the skills you need to progress. Alignment problems are a great way to learn dynamic programming and will allow you to move onto some of these other problems (like mass spec and HMMs) more reasonably (at least, in my experience!) Good luck!

eesmith 7y ago
A closer reading shows that I got tripped up by what "residue" means. But I'm not sure the author of the question got it right either? At the very least, I'm confused by it. The first paragraph of the expanded question text has: "every pair of adjacent amino acids has lost one molecule of water, meaning that a polypeptide containing n amino acids has had n−1 water molecules removed" The second paragraph has: "Thus, the mass of a protein is the sum of masses of all its residues plus the mass of a single water molecule." The fifth paragraph has: "The mass of a protein is the sum of the monoisotopic masses of its amino acid residues plus the mass of a single water molecule" And the monoisotopic mass table says "Note: the monoisotopic mass of water is considered to be 18.01056 Da." So I thought that the water molecule was important in the calculation. However, the last paragraph (which I only now closely read) says it isn't important, with "In the following several problems on applications of mass spectrometry, we avoid the complication of having to distinguish between residues and non-residues by only considering peptides excised from the middle of the protein. This is a relatively safe assumption because in practice, peptide analysis is often performed in tandem mass spectrometry." Since it didn't mention "water", and instead used the specialist term "residue", I missed the connection earlier. That said, the text seems to use "residue" inconsistently. There's the definition "a residue is a molecule from which a water molecule has been removed; every amino acid in a protein are residues except the leftmost and the rightmost ones." but there's also the usage: "the mass of a protein is the sum of masses of all its residues plus the mass of a single water molecule" Surely that should be "the mass of a protein is the sum of masses of all its residues plus the mass of its leftmost and rightmost amino acids minus the mass of a single water molecule", yes? So I looked up the definition of "amino acid residue". It appears to be https://goldbook.iupac.org/terms/view/A00279 https://goldbook.iupac.org/terms/view/A00279 "α-Amino-acid residues are therefore structures that lack a hydrogen atom of the amino group (–NH–CHR–COOH), or the hydroxyl moiety of the carboxyl group (NH2–CHR–CO–), or both (–NH–CHR–COO–); all units of a peptide chain are therefore amino-acid residues". https://en.wikipedia.org/wiki/Protein_sequencing#Whole-mass_determination https://en.wikipedia.org/wiki/Protein_sequencing#Whole-mass_... also agrees that "residue" includes the two amino acids at the ends, saying "The protein’s whole mass is the sum of the masses of its amino-acid residues plus the mass of a water molecule and adjusted for any post-translational modifications" Which means ... I don't think the author uses the term "residue" correctly? Or, more likely, I'm confused by the specialist terminology. Can someone clear up my confusion?
- ihunter2839 7y ago
  Re: the mass of a protein is the sum of all its residues plus the mass of a single water molecule / your second definition, they are equivalent. You could re-write you second version as (sum of all residues minus left and right most) + (sum of left and right residues + two molecules of water) - (one molecule of water) === sum of residues + one water molecule. (The key is that residues are created whenever a molecule of water is expelled. In theory, you can expel exactly one water molecule from each amino acid to create a residue, with one hydrogen from the amine group and the hydroxl from the carboxylic acid. In reality, it takes two amino acids to start the process of peptide synthesis, and each aa contributes only one part (either the proton or the hydroxl group) of the theoretically expelled water molecule. In reality its not even a single water molecule, as the hydroxyl group is going to pick up a spare proton from solution and the extra proton on the amine will get pick up by gawd knows what) <-- Downright wrong (at least, in regards to its importance to residues.). The condensation is connected in this instance but not in all instances of residues. I think the usage is more clear if you look at some of the other examples in the biochemistry section of the wiki page "...a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. One might say, "This protein consists of 118 amino acid residues" or "The histidine residue is considered to be basic because it contains an imidazole ring." (https://en.wikipedia.org/wiki/Residue_(chemistry) https://en.wikipedia.org/wiki/Residue_(chemistry))
- mnemonicsloth 7y ago
  Think of the normal meaning of the word. The residue is what's left over after whatever was going to happen has finished happening. For amino acids, the interesting thing is that they get joined into chains that fold up into proteins (which do all the work). The residues after that happens looks like this: R O R O H | || H | || H ----- N - C - C --------- N - C - C ----------- N etc H H The lines - and | are chemical bonds. The Oxygens are double bonded. N= Nitrogen, C=Carbon, O=Oxygen. The R is one of 20 different chemical groups called side chains that make each amino acid different. When the amino acids are isolated (not chained) the double-bonded carbon on the right carries an extra OH group. The whole right-hand carbon is often written COOH. The nitrogen on the left hand side of each amino acid carries an extra H. As part of the process that joins the amino acids together, the OH on the left and the H on the right pair off to form water. This is called condensation, and it happens at every junction between two acids. So if there are n amino acids, there are n-1 junctions and n-1 water molecules that were present (in aggregate) in the constituent amino acids that don't make it into the final protein chain. Note, though, that one of the methods of chopping up protein chains is adding the water molecules back again, so you should know exactly what you're looking if you want to count masses precisely. Jeez. Didn't mean to write all that. Hope it helps.
eesmith 7y ago
I was thinking about this some more. You wrote "after the initial ionization phase of mass spectroscopy". In high school I tried to build a mass spectrometer. It didn't work - I couldn't get a high enough vacuum, and a few years later as a physics undergrad did I find that that was only one of several problems I had. It was fun to try though. But I do know that the ionized particle has a charge, and that electron affects the overall mass, by about 1/1836 Dalton . That's 0.00054 Dalton, while the table lists masses down to even higher accuracy, like 71.03711 . The example output gives a value down to 3 decimal digits, so at that precision there's a 50% chance that the electron mass will affect the result. Isn't this problem therefore implicitly teaching an excessive trust in significant digits? Now, I suspect that the mass spectrometers they use aren't that accurate. But it's bugging me now. As mbreese wrote elsewhere here, I'm (clearly) reading too much into the problem. I don't think bioinformatics is the right field for me.
- ihunter2839 7y ago
  IANAP (really, IA(BARELY)AB), but I am not exactly clear where these additional electrons are sneaking in. Either way, I'm not sure the change would be significant enough to move the spectral peak outside of the range for a specific residue. There are lots of false peaks, and a lot of pre / post processing goes into managing those complexities. Re bioinformatics /residues / lingo / life - bioinformatics is a catch all term for a set of loosely related tools being applied across the full field of disciplines. The early pioneers in bioinformatics (like Pevzner himself) were all physicists and electrical engineers who moved into the realm of biology. Your exact terminology is generally dependent on the specific problem you are solving and may be slightly different that the more general uses of the same words. Either way, I hope that if you are interested in the underlying topics that bioinformatics deals with, you won't let some issues in vernacular trip you up!
  - eesmith 7y ago
    https://en.wikipedia.org/wiki/Dalton_(unit)#Measurement https://en.wikipedia.org/wiki/Dalton_(unit)#Measurement says "Although relative atomic masses are defined for neutral atoms, they are measured (by mass spectrometry) for ions: hence, the measured values must be corrected for the mass of the electrons that were removed to form the ions, and also for the mass equivalent of the electron binding energy," I tried to find some place which worked this out more than my earlier calculation. The closest was https://www.waters.com/webassets/cms/library/docs/720000807en.pdf https://www.waters.com/webassets/cms/library/docs/720000807e... under the entry for "Molecular ion" > The mass of the molecular ion corresponds to the nominal or monoisotopic mass of the molecule, with the mass of the electron added or lost usually consequential. However, I can't help but think that last word should be "inconsequential." I did find https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.8478#rcm8478-fig-0002 https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.8478#rc... which shows it's possible to measure the difference between ¹⁶O¹⁸O⁺⁺ and ¹⁷O⁺ ("The interference of ¹⁶O¹⁸O⁺⁺ can be detected 0.002 mass units before the larger ¹⁷O⁺ peak starts.") That must be due to binding energy as the naive charge/mass ratio is identical. That's only 4x more than the 0.00054 mass units I estimated for an electron. I looked at some of the other example problems. I do not think I am interested in this field. Thank you for your exchange of information.

eesmith 7y ago

A closer reading shows that I got tripped up by what "residue" means. But I'm not sure the author of the question got it right either? At the very least, I'm confused by it. The first paragraph of the expanded question text has: "every pair of adjacent amino acids has lost one molecule of water, meaning that a polypeptide containing n amino acids has had n−1 water molecules removed" The second paragraph has: "Thus, the mass of a protein is the sum of masses of all its residues plus the mass of a single water molecule." The fifth paragraph has: "The mass of a protein is the sum of the monoisotopic masses of its amino acid residues plus the mass of a single water molecule" And the monoisotopic mass table says "Note: the monoisotopic mass of water is considered to be 18.01056 Da." So I thought that the water molecule was important in the calculation. However, the last paragraph (which I only now closely read) says it isn't important, with "In the following several problems on applications of mass spectrometry, we avoid the complication of having to distinguish between residues and non-residues by only considering peptides excised from the middle of the protein. This is a relatively safe assumption because in practice, peptide analysis is often performed in tandem mass spectrometry." Since it didn't mention "water", and instead used the specialist term "residue", I missed the connection earlier. That said, the text seems to use "residue" inconsistently. There's the definition "a residue is a molecule from which a water molecule has been removed; every amino acid in a protein are residues except the leftmost and the rightmost ones." but there's also the usage: "the mass of a protein is the sum of masses of all its residues plus the mass of a single water molecule" Surely that should be "the mass of a protein is the sum of masses of all its residues plus the mass of its leftmost and rightmost amino acids minus the mass of a single water molecule", yes? So I looked up the definition of "amino acid residue". It appears to be https://goldbook.iupac.org/terms/view/A00279 https://goldbook.iupac.org/terms/view/A00279 "α-Amino-acid residues are therefore structures that lack a hydrogen atom of the amino group (–NH–CHR–COOH), or the hydroxyl moiety of the carboxyl group (NH2–CHR–CO–), or both (–NH–CHR–COO–); all units of a peptide chain are therefore amino-acid residues". https://en.wikipedia.org/wiki/Protein_sequencing#Whole-mass_determination https://en.wikipedia.org/wiki/Protein_sequencing#Whole-mass_... also agrees that "residue" includes the two amino acids at the ends, saying "The protein’s whole mass is the sum of the masses of its amino-acid residues plus the mass of a water molecule and adjusted for any post-translational modifications" Which means ... I don't think the author uses the term "residue" correctly? Or, more likely, I'm confused by the specialist terminology. Can someone clear up my confusion?

ihunter2839 7y ago
Re: the mass of a protein is the sum of all its residues plus the mass of a single water molecule / your second definition, they are equivalent. You could re-write you second version as (sum of all residues minus left and right most) + (sum of left and right residues + two molecules of water) - (one molecule of water) === sum of residues + one water molecule. (The key is that residues are created whenever a molecule of water is expelled. In theory, you can expel exactly one water molecule from each amino acid to create a residue, with one hydrogen from the amine group and the hydroxl from the carboxylic acid. In reality, it takes two amino acids to start the process of peptide synthesis, and each aa contributes only one part (either the proton or the hydroxl group) of the theoretically expelled water molecule. In reality its not even a single water molecule, as the hydroxyl group is going to pick up a spare proton from solution and the extra proton on the amine will get pick up by gawd knows what) <-- Downright wrong (at least, in regards to its importance to residues.). The condensation is connected in this instance but not in all instances of residues. I think the usage is more clear if you look at some of the other examples in the biochemistry section of the wiki page "...a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. One might say, "This protein consists of 118 amino acid residues" or "The histidine residue is considered to be basic because it contains an imidazole ring." (https://en.wikipedia.org/wiki/Residue_(chemistry) https://en.wikipedia.org/wiki/Residue_(chemistry))
mnemonicsloth 7y ago
Think of the normal meaning of the word. The residue is what's left over after whatever was going to happen has finished happening. For amino acids, the interesting thing is that they get joined into chains that fold up into proteins (which do all the work). The residues after that happens looks like this: R O R O H | || H | || H ----- N - C - C --------- N - C - C ----------- N etc H H The lines - and | are chemical bonds. The Oxygens are double bonded. N= Nitrogen, C=Carbon, O=Oxygen. The R is one of 20 different chemical groups called side chains that make each amino acid different. When the amino acids are isolated (not chained) the double-bonded carbon on the right carries an extra OH group. The whole right-hand carbon is often written COOH. The nitrogen on the left hand side of each amino acid carries an extra H. As part of the process that joins the amino acids together, the OH on the left and the H on the right pair off to form water. This is called condensation, and it happens at every junction between two acids. So if there are n amino acids, there are n-1 junctions and n-1 water molecules that were present (in aggregate) in the constituent amino acids that don't make it into the final protein chain. Note, though, that one of the methods of chopping up protein chains is adding the water molecules back again, so you should know exactly what you're looking if you want to count masses precisely. Jeez. Didn't mean to write all that. Hope it helps.

eesmith 7y ago

I was thinking about this some more. You wrote "after the initial ionization phase of mass spectroscopy". In high school I tried to build a mass spectrometer. It didn't work - I couldn't get a high enough vacuum, and a few years later as a physics undergrad did I find that that was only one of several problems I had. It was fun to try though. But I do know that the ionized particle has a charge, and that electron affects the overall mass, by about 1/1836 Dalton . That's 0.00054 Dalton, while the table lists masses down to even higher accuracy, like 71.03711 . The example output gives a value down to 3 decimal digits, so at that precision there's a 50% chance that the electron mass will affect the result. Isn't this problem therefore implicitly teaching an excessive trust in significant digits? Now, I suspect that the mass spectrometers they use aren't that accurate. But it's bugging me now. As mbreese wrote elsewhere here, I'm (clearly) reading too much into the problem. I don't think bioinformatics is the right field for me.

ihunter2839 7y ago
IANAP (really, IA(BARELY)AB), but I am not exactly clear where these additional electrons are sneaking in. Either way, I'm not sure the change would be significant enough to move the spectral peak outside of the range for a specific residue. There are lots of false peaks, and a lot of pre / post processing goes into managing those complexities. Re bioinformatics /residues / lingo / life - bioinformatics is a catch all term for a set of loosely related tools being applied across the full field of disciplines. The early pioneers in bioinformatics (like Pevzner himself) were all physicists and electrical engineers who moved into the realm of biology. Your exact terminology is generally dependent on the specific problem you are solving and may be slightly different that the more general uses of the same words. Either way, I hope that if you are interested in the underlying topics that bioinformatics deals with, you won't let some issues in vernacular trip you up!
- eesmith 7y ago
  https://en.wikipedia.org/wiki/Dalton_(unit)#Measurement https://en.wikipedia.org/wiki/Dalton_(unit)#Measurement says "Although relative atomic masses are defined for neutral atoms, they are measured (by mass spectrometry) for ions: hence, the measured values must be corrected for the mass of the electrons that were removed to form the ions, and also for the mass equivalent of the electron binding energy," I tried to find some place which worked this out more than my earlier calculation. The closest was https://www.waters.com/webassets/cms/library/docs/720000807en.pdf https://www.waters.com/webassets/cms/library/docs/720000807e... under the entry for "Molecular ion" > The mass of the molecular ion corresponds to the nominal or monoisotopic mass of the molecule, with the mass of the electron added or lost usually consequential. However, I can't help but think that last word should be "inconsequential." I did find https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.8478#rcm8478-fig-0002 https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.8478#rc... which shows it's possible to measure the difference between ¹⁶O¹⁸O⁺⁺ and ¹⁷O⁺ ("The interference of ¹⁶O¹⁸O⁺⁺ can be detected 0.002 mass units before the larger ¹⁷O⁺ peak starts.") That must be due to binding energy as the naive charge/mass ratio is identical. That's only 4x more than the 0.00054 mass units I estimated for an electron. I looked at some of the other example problems. I do not think I am interested in this field. Thank you for your exchange of information.