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I'm interested in the most abundant proteins inside cells by total mass of the protein (for example average for a whole human or for specific organs/tissues/cell lines).

It is quite easy to find that the largest % by mass in the human body is collagen (25 to 35% of total body protein). Collagen is an extracellular protein; finding the same info for intracellular proteins has been surprisingly difficult. Finding what is the second largest %, or a top 10 list, has also been difficult.

In the process of searching, I found PaxDb which lists protein abundance by "ppm", or counts divided by the total counts. It is quite hard to convert that to % by mass - it would be necessary to know the molecular mass of every protein (for example by matching them with entries in UniProt), and then multiply count by molecular mass. Another resource which seems to have a lot of data is PeptideAtlas, but I can't tell how to extract either counts or masses from that.

Is there a canonical list of (eg) top 10 or top 100 intracellular proteins by mass in a whole human? How about the same by organ/tissue?

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    $\begingroup$ I can’t see why a scientist would prefer a mass-based, rather than a molar value, except, perhaps for which proteins are likely to correspond to spots on a 2D gel. I seem to remember that EF-Tu/EF-T1 was one of the stars (but that was in my field of interest). You could try searching the 2D gel literature for that sort of thing, however it will probably miss the very basic ribosomal proteins, which are analysed on a different gel system. But, really, the values for the “average human cell” would seem of interest only to stamp collectors. Have you no context? $\endgroup$
    – David
    Sep 11, 2023 at 18:46
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    $\begingroup$ Similar to David's comment, you want to make sure you're avoiding the XY problem: what is the underlying problem you're trying to solve? It's possible there is a better solution to the underlying problem than the one you've come up with. $\endgroup$
    – Bryan Krause
    Sep 11, 2023 at 18:55
  • $\begingroup$ @David I'm interested in physical properties which would be determined, in a mixture, by the predominant components by mass not count (think stuff like Trp fluorescence spectroscopy or XANES). I'd like to pick a couple of single proteins as models for simplicity, but it makes sense to pick ones which would mostly determine the results when measuring an intact whole cell as well. $\endgroup$
    – Alex I
    Sep 11, 2023 at 19:11
  • $\begingroup$ @AlexI I'm not familiar with that field, what percent by mass would the predominant component need to be for it to be considered "predominant enough"? And why would the mass of the rest of the protein matter for Trp fluorescence spectroscopy? $\endgroup$
    – Bryan Krause
    Sep 11, 2023 at 19:23
  • $\begingroup$ @BryanKrause Just using that as an example, my actual motivation is a different spectroscopic technique. It would be "% of all Trp" of course, but as long as the fraction of that in aa sequence of different proteins is similar, "% of protein mass" is a pretty good substitute $\endgroup$
    – Alex I
    Sep 11, 2023 at 19:28

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