in general is there some reference that describes each field in this table?

Dear Colin,

One more comment to add to Andreas' reply; it also assumes that most proteins do not change in a comparative analysis of labeled cells undergoing condition A,  vs cells not undergoing any condition, condition B.  I believe that the normalization of the data may include the fact that most proteins identified have H/L :1

If the MS1 H/L intensities for peptides reported by MaxQuant are compared to the intensities in eg., your RAW files, there is a very good correlation with exception of, as Andreas noted, the outliers that exhibit spectrum with heterogeneity eg., split peaks.

Best,

Hediye.

Thanks a lot for the answers, very helpful.

Best wishes

Colin

This value is calculated from three separate ratios:

Ratio H(heavy treated)/ light treated protein group

Ratio H/L modified peptide

Ratio H/L unmodified counterpart peptide