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.