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I am reading some journal papers about the proteome of certain brain structures. In these papers, they used mass spectrometry to identify the proteins that were present in the brain structure as well as their abundance. In one paper, they performed high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. In another paper, they performed nanoLC-high resolution mass spectrometry and used a tandem mass tags (TMT)-based labelling approach.

I am interested in finding out whether certain proteins are expressed in these brain structures. I have downloaded the supplementary tables from the papers that gives information about average level (as they had several samples of the brain structure) of each protein found in that brain structure. However, I am new to analysing mass spectrometry data and I unsure about what are the units of mass spectrometry data. I could not find anything regarding the units of the data in the papers or their supplementary tables.

In general, I was wondering for mass spectrometry data, what are the units used to describe the abundance of a protein in a sample? For example, in RNA-Seq data when quantifying the number of gene transcripts you have normalised read counts such as RPKM/TPM. These values can be averaged across samples such that you get the average RPKM/TPM value for a gene.

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  • $\begingroup$ Can't you just weigh the sample first? $\endgroup$
    – DKNguyen
    Feb 13, 2022 at 2:24
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    $\begingroup$ You really need to refer to either a concrete example in a paper that we can interpret, or state precisely what it is you want to do — compare proteins in one experiment, from different experiments, determine absolute concentrations or what? The “data” is obviously a spectrometries trace in which you can measure the height of a peak, or the area under it. This obviously has no units as such. $\endgroup$
    – David
    Feb 13, 2022 at 16:42
  • $\begingroup$ @David I am trying to interpret the data from this paper (sciencedirect.com/science/article/pii/S2211124721012572). In Supplementary Table 1 of this paper (where they show the average levels of each protein in the synaptosomes), I am trying to figure out what the unit of protein abundance is. $\endgroup$
    – ceno980
    Feb 13, 2022 at 20:44
  • $\begingroup$ @ceno980 — I see you have accepted an answer, but I'll have a look at it tomorrow and add any additional comments I may have. $\endgroup$
    – David
    Feb 13, 2022 at 21:05
  • $\begingroup$ @David Thank you $\endgroup$
    – ceno980
    Feb 13, 2022 at 22:11

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I think MS data, like other spectroscopy and chromatography data, is usually quantified by comparing peak areas (in arbitrary units) to those of a quantitative standard. So the Y axis is just the intensity of the signal, often which doesn't display its direct experiment readout units (like current or voltage). In other words, you need the results of control or calibration experiments extraneous to the raw MS data.

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  • $\begingroup$ I don't think the units are 'arbitrary' per se, but rather are the units that result from integrating the signal with respect to time. If the units of the variables are not arbitrary, which for physical units they are not, then the definite integral's units are not arbitrary either. For someone interested in the concentration of an analyt, it is true that the (usually linear) calibration converts this area measure into units of concentration (or similar) such as Molar. That aside, I think your answer cuts pretty cleanly to the point (+1). $\endgroup$
    – Galen
    Feb 14, 2022 at 16:49

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