Raw measurement files were analyzed with MaxQuant 1.5.2.8 standard settings (Cox and Mann 2008, PMID:19029910), except for LFQ quantitation, and match between run option was activated. Peptides were identified by comparison to the translated Ensembl transcript database (release 79) of D. melanogaster and the S. cerevisiae protein database. Protein abundance was measured using the MaxLFQ method of label-free quantitation (Cox et al., 2014, PMID:24942700). Known contaminants, protein groups only identified by site, and reverse hits of the MaxQuant results were removed. Only unique peptide intensities for each protein group were used for protein quantification.

For the purposes of analysis, imputation was performed to replace missing normalized intensity values for a given protein. Missing values were drawn from a distribution calculated with the logspline R package (https://cran.r-project.org/package=logspline). For cases where three or more replicates were measured, the mean of the measured replicates was used as the mean parameter of the distribution. Otherwise, the average of the two neighboring time points was used. In cases of no measured values in neighboring time points or for proteins measured only in one replicate with no surrounding values, a fixed value of 22.5 close to the limit of detection (LOD) was used.

The original publication reported expression values in four biological replicates for each sample using log2-transformed values. FlyBase reports the geometric mean of these four sample replicates, without the log2 transformation. For ease of display, FlyBase values are also divided by a million. Both the original values and FlyBase processed values are in arbitrary units.