I am a graduate student majoring in genome-informatics.
Recently, I am combining genome, transcriptome and proteome data of LC-MS/MS.
Quantitative proteome information differs from other omic data sets.
Therefore, I am struggling to understand its characteristics and experimental procedures.
As far as I know, LC-MS/MS uses HPLC to separate peptides according to size. After the separation, each elute (fraction) is analyzed by MS/MS to get peptide intensity. The first quantile normalization is applied to reduce systematic error between different fractions since peptides in fractions may have different intensity.
Is what I know right? I don't understand why quantile normalization is applied since every fraction is likely to have different peptide components.
I also would like to know how to calculate S2I. I already read the Savitski, M. M.'s paper (J. Am. Soc. Mass Spectrom. 2010, 21, 1668–1679).
The S2I is to estimate peptide purity (the lower the more comtaminated). The formula is basically the sum of precursor ion intensity/the sum of total ion intensity within isolated peak window. I am very confused because WIKI says that ion intensity is an arbitrary unit which all peptides may different ion intensity though they have same molecular abundance
Please explain the calculation method of S2I.