Fig. 1

PIT identifies additional proteins in Ae. aegypti cells compared to ‘conventional’ proteomics. a Overview of the PIT pipeline. In ‘conventional’ proteomics (i), proteins detected by high-throughput LC-MS/MS from Ae. aegypti cell extracts are identified by comparison to mass spectra computationally predicted from protein or transcript annotations on the Ae. aegypti reference genome. (Annotated transcripts are in silico translated prior to mass spectra prediction). PIT identifies additional proteins by using RNA-seq to identify transcripts in RNA samples matched to protein isolates (ii). Transcripts are assembled de novo using Trinity software, translated in silico, and used for mass spectra prediction for peptide identification. From a single experimental sample, proteins are identified without the need for an annotated reference genome, and transcript abundance can be inferred from RNA-seq data. b Total unique proteins (i) and proteins with at least two recorded peptides (ii) identified in Aag2 cells based on the Ae. aegypti reference genome protein or transcript annotations, or using PIT. Percentages indicate the proportion of proteins identified only by PIT. c BLAST analysis of the PIT-identified proteome. Hits were mapped against the Ae. aegypti [taxid 7159], Culex quinquefasciatus [taxid 7176] (Culex) or Drosophila melanogaster [taxid 7227] (Drosophila) Ref-Seq databases. A subset of hits did not match annotated genes from these dipteran insects (non-insect). (i) Total PIT proteome, (ii) Translated ORFs from Trinity transcripts matched with at least two peptides