Table 1 Details of datasets

Dataset A

Pride ID—PXD002952

3 samples of 65% human, 30% yeast, 5% E. coli peptides (Control)

3 samples of 65% human, 15% yeast, 20% E. coli peptides (Test)

Reference set—a well-defined dataset with predictable quantification

Dataset B

In vitro experiments carried out in this study

3 samples of K562/S cells (Control)

3 samples K562/S + IM cells (Test)

Study set to check comparability of observations in defined (A) versus undefined (B) datasets

Dataset C

In vitro experiments carried out in this study

12 samples of K562/S cells (Control)

12 samples K562/S + IM cells (Test)

Larger dataset (C) to check the application of observations from small dataset (B)

Dataset D

In vitro experiments carried out in this study

12 samples of K562/S + IM cells (Control)

12 samples K562/R cells (Test)

Larger dataset (D) to check the consistency of observations in independent large datasets

Dataset E

Pride ID—PXD006106

10 samples of untreated HeLa Kyoto cells (Control)

10 samples of formaldehyde treated HeLa Kyoto cells (Test)

Validation set to check the consistency of observations in independent large datasets

Dataset F

Pride ID—PXD000672

18 non-tumorous kidney tissue samples (Control)

18 tumorous kidney tissue samples (Test)

Validation set to check the consistency of observations in independent large datasets