Summary of proteomics data.

Data are presented for species individually and for the total of all three species combined. The protein discovery (PD) analysis was performed at a protein identification threshold of 90%, the highest quality (HQ) data set was compiled at a threshold of 99%. For spectra, numbers are given before (‘raw’) and after (‘clean’) removal of known contaminants. All other numbers were obtained from cleaned spectra only.
1Proteins matching a sequence in the Ophrys reference transcriptome. In the HQ data set, 115 were 454 singleton reads, 4 Sanger singleton reads, 388 Solexa contigs, 343 pyrosequencing isotigs and 753 combined 454/Solexa contigs. Among these 1603 HQ orchid proteins, no peptide matched translations from different strands, and only 11 proteins (0.7%) had peptides matching to two reading frames of the same transcript strand (in each case due to a single frame shift).
2Proteins not matching any Ophrys transcript, but with SwissProt and/or TAIR9 database hit.