## Evaluation of the confidence in the protein pair-wise measured correlation coefficient.

Fig 2A hierarchical clustering of the protein pair-wise correlation coefficient for a β = 1; in Fig 2B, correlation coefficient evaluated after intensity randomisation for a β = 1. Fig 2C Distribution of the correlation coefficient from direct correlation in turquoise (extracted from Fig 2A) or after intensity randomisation in blue (extracted from Fig 2B). Fig 2D is the ratio false positive hits versus measurements obtained in the dataset. A correlation coefficient of 0.754 and above indicates positive correlation while -0.728 and less for negative correlation corresponds to a ratio of false positive below 5%. In Fig 2E the same measurements as in 2C in the case of a soft threshold β = 10. In Fig 2F, a false positive rate equal to or below 5% corresponds to a value of 0.0993 and above.