An interaction network of RNA-binding proteins involved in Drosophila oogenesis

Prashali Bansal; Johannes Madlung; Kristina Schaaf; Boris Macek; Fulvia Bono

All the samples were prepared in biological triplicates and the resulting spectra were searched against the Drosophila melanogaster proteome database (Fig. 1a, Fig. S2a ). For confident identification of proteins and . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.08.899146 doi: bioRxiv preprint 12 accurate intensity-based Label-Free Quantification (LFQ), we processed the raw data using the MaxLFQ module of the MaxQuant software (71, 73) . Additionally, we activated the "matching between runs" algorithm to quantify unidentified or un-sequenced peptides in the samples, by transferring peptide identifications among replicates. The global analysis of the proteomes resulted in the identification of 15,005 peptides mapping to 1878 protein groups, at a FDR of 1% at the peptide and protein level. Of these, 1841 unique protein groups were quantified in at least one of the 21 samples, which account for 87.5% of the total ovary proteome of Drosophila (84) . The average correlation within replicates ranged from 0.71 (Glo) to 0.92 (Hrp48), suggesting overall good reproducibility of the data (Fig. 1c ). In addition, the visualization of LFQ intensities of all the samples as a heat map demonstrates that all the baits were consistently enriched (Fig. S2c ). The replicate profiles looked largely similar, with only minor differences. However, the number of proteins quantified with each bait varied highly, as marked by the absence of information in the heat map ( Fig. S2c ).