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> Or, more likely, I'm confused by the specialist terminology. Can someone clear up my confusion? I think you're just reading too much into the problem. The te

> Or, more likely, I'm confused by the specialist terminology. Can someone clear up my confusion? I think you're just reading too much into the problem. The terminology can be a bit daunting and it can be very hard for bioinformatics people to realize just how much specialist terminology we end up using. I mean, we have both computer science and molecular biology jargon that we use every day. It's sometimes hard to recognize just how much assumed knowledge there is in this field. Unfortunately, bioinformatics is full of edge cases like this. In this example, if you're talking about the size of a full protein, you need to add the mass of a water (to account for the lack of a bond at the N and C terminus). However, if you're talking about the size of a peptide fragment (a sub-sequence), then you don't need to account for the extra water molecule [0]. And as the explanation says -- peptide identification is the most common use-case for this analysis, so we'll just use that. This is also why the table lists the "residue" weights -- because it's easier to calculate the `sum(residue_weight) + water` as opposed to `sum(amino_acid_weight) - (n-1) * water`. I think the extra explanation isn't entirely clear, but I wouldn't get hung up on that part or let that bother you too much. The problem really boils down to: calculate a weighted sum of a string using these weights for the letters. That's it... no more, no less. Congrats on working through the exercise. This is honestly great resource for learning about the field from a coding perspective. As others have mentioned, this is from the people who literally wrote the book about much of the field. [0] Note: In the protein, you aren't actually adding an intact water molecule itself, but accounting for the extra H at one end, and an extra OH at the other end. Which is the same weight as HOH, or 18.01056 Da.

eesmith 7y ago
Yes, I'm likely reading too much into it. I think it means that I don't want to work in bioinformatics, if there's such ambiguity over what seems to be a basic term. Does the term "residue" include the ex-amino acid components at the end of the protein? The text is clear that it doesn't. The popup says that "a residue is a molecule from which a water molecule has been removed". But it's internally inconsistent, and the IUPAC definition says that it does include the ends.
- pdm55 7y ago
  I would follow the IUPAC Gold book definition. That is written by a committee that seeks exact wording. The other source seems a little sloppy with their definition. As to whether you might consider working in the field of bioinformatics, I can only pass on a comment from a researcher in the field. She says that they are being "swamped with data". Lots of data, but a lack of computer nerds to work on it. PS I also noticed the reference to post-translational modification in one of your comments. This is one of the factors that makes for the amazing variety in protein/enzyme functioning. Humans have about 20 000 genes to encode about 75 000 different enzymes, plus a multitude of structural, storage, hormonal, etc. proteins. So you can see that translation of the gene is only the beginning of the story; post-translational modifications are needed. https://www.sciencedirect.com/topics/neuroscience/posttranslational-modification https://www.sciencedirect.com/topics/neuroscience/posttransl... It's an unlimited area of study - one I stepped out of and wish I had stayed in. Of course, to make any sense of a complex system, one has to concentrate on a small part of it. Focus on what takes your interest (and you can get paid for).
  - eesmith 7y ago
    Years ago I got the advice to not go into software development for science. The reasoning was that those companies are mostly run by people with PhDs who took 6 years to get their degree, and getting paid a pittance. These people find it hard to believe that a non-PhD software developer should be paid significantly more than a PhD. I don't know if it's true, but when I see "Lots of data, but a lack of computer nerds to work on it." ... I read it as saying there's no money to hire those computer nerds. The same person advised me that the software developers who go into science often do so for the love of the topic, and willing to be paid less. I don't think I can get that interested in bioinformatics.
- asjo 7y ago
  > I think it means that I don't want to work in bioinformatics, if there's such ambiguity over what seems to be a basic term. Yes, biology is a mess of exceptions, "good enough" and "hey, it works". It does have its charm as well, though. One of the first things I learned from that world is that if you ask a microbiologist if something is always the case, the answer will be "Yes" if it is true more than ~80% of the time.

eesmith 7y ago

Yes, I'm likely reading too much into it. I think it means that I don't want to work in bioinformatics, if there's such ambiguity over what seems to be a basic term. Does the term "residue" include the ex-amino acid components at the end of the protein? The text is clear that it doesn't. The popup says that "a residue is a molecule from which a water molecule has been removed". But it's internally inconsistent, and the IUPAC definition says that it does include the ends.

pdm55 7y ago
I would follow the IUPAC Gold book definition. That is written by a committee that seeks exact wording. The other source seems a little sloppy with their definition. As to whether you might consider working in the field of bioinformatics, I can only pass on a comment from a researcher in the field. She says that they are being "swamped with data". Lots of data, but a lack of computer nerds to work on it. PS I also noticed the reference to post-translational modification in one of your comments. This is one of the factors that makes for the amazing variety in protein/enzyme functioning. Humans have about 20 000 genes to encode about 75 000 different enzymes, plus a multitude of structural, storage, hormonal, etc. proteins. So you can see that translation of the gene is only the beginning of the story; post-translational modifications are needed. https://www.sciencedirect.com/topics/neuroscience/posttranslational-modification https://www.sciencedirect.com/topics/neuroscience/posttransl... It's an unlimited area of study - one I stepped out of and wish I had stayed in. Of course, to make any sense of a complex system, one has to concentrate on a small part of it. Focus on what takes your interest (and you can get paid for).
- eesmith 7y ago
  Years ago I got the advice to not go into software development for science. The reasoning was that those companies are mostly run by people with PhDs who took 6 years to get their degree, and getting paid a pittance. These people find it hard to believe that a non-PhD software developer should be paid significantly more than a PhD. I don't know if it's true, but when I see "Lots of data, but a lack of computer nerds to work on it." ... I read it as saying there's no money to hire those computer nerds. The same person advised me that the software developers who go into science often do so for the love of the topic, and willing to be paid less. I don't think I can get that interested in bioinformatics.
asjo 7y ago
> I think it means that I don't want to work in bioinformatics, if there's such ambiguity over what seems to be a basic term. Yes, biology is a mess of exceptions, "good enough" and "hey, it works". It does have its charm as well, though. One of the first things I learned from that world is that if you ask a microbiologist if something is always the case, the answer will be "Yes" if it is true more than ~80% of the time.