Hi, I am looking at MaxQuant (MQ) quantification of protein ids across several samples. I am using unique + razor peptides, which is provided as a list in proteinGroups.txt, then summing the contributions of these peptides (Intensities) for each protein id in each sample from peptide.txt. While the calculated sums for each protein id in each sample are generally very close to that described in proteinGroups.txt, there are some small differences. At first glance, it seems as if this could be due to some rounding function, but if it is, this is not applied consistently.

As an example, protein x across 16 samples is described/calculated as:

proteinGroups.txt

165800.0,2645200.0,2931200.0,3259200.0,1089700.0,1442800.0,1716700.0,5423000.0,

0.0,165790.0,524820.0,2698200.0,0.0,248370.0,986320.0,2062400.0.

peptides.txt

165800.0,2645250.0,2931200.0,3259280.0,1089700.0,1442841.0,1716720.0,5423080.0,

0.0,165790.0,524820.0,2698180.0,0.0,248365.0,986317.0,2062380.0.

In this example you can see rounding in some values, but not in others (e.g. for element {sample} 10 in the list).

Can anyone throw light onto how these small (but annoying!) differences arise?