The developmental proteome applied label-free quantitative methods (LFQ) to measure protein expression throughout development. Expression values were measured for protein groups (each consisting of a set of proteins matching a set of observed peptides). Each protein group was defined by the authors as a set of corresponding mRNA transcripts (FBtr IDs); the transcript IDs given were used to map protein groups to corresponding FlyBase genes. In most cases, protein groups mapped one-to-one with genes. However, in some cases, a protein group was defined by a set of observed peptides mapping to several genes; in these cases, the measured expression values were assigned by FlyBase to all genes comprised by the protein group. In other cases, a gene had several associated protein groups, each protein group corresponding to a distinct set of protein isoforms; for these genes, FlyBase captured only the expression values from the protein group with the highest average expression value across all samples of a given dataset (embryogenesis or life cycle). Please consult the original publication to obtain expression data for additional protein isoforms of a given gene. For three protein groups, the transcripts reported corresponded to older gene models that have since been split into distinct genes; as these data confound multiple genes, they were discarded. The attached file details the protein group-to-gene assignment by FlyBase.

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.

Note also that in rare cases (~0.1%), the reported expression value was less than the reported "limit of detection" (LOD); in such cases, the LFQ value was set equal to 3858948 (the value used by the authors to replace null values when the protein was not detected in a given sample).