Tissue Whole Hemolymph Solid tissue Brain Crop (foregut) Eye Galea Hemolymph Intestine Leg (front) Leg (mid) Leg (rear) Mandibular gland Mouth part Muscle Ocellus Mucus gland Testis Spermatheca Abdomen Antenna Fat body Ovary Salivary Gland Thorax Wing Poison sac Sternite Tergite Pollen Rectum (hindgut) Salivary gland (post-cerebral) Salivary gland (thoracic) Ventriculus (midgut) all all all all all all all all all all all all all all all all all Drone Drone Queen Worker Worker Worker Worker Worker Worker Worker, Drone Worker, Queen Worker, Queen Worker, Queen - adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult adult - Chan et al. BMC Genomics 2011, 12:290 http://www.biomedcentral.com/1471-2164/12/290 Table 1 Honey bee castes and tissue samples in PeptideAtlas Caste Indeterminate Worker Worker Developmental Stage egg larval instars 1-5 larval instars 1-5 remain as it is difficult to discern which are the result of sequencing errors from real SNPs or gene duplications. This new protein list may be downloaded at the Pepti- deAtlas honey bee download area. Construction of PeptideAtlas All raw data were converted to mzML [18] using the msconvert tool from Proteowizard [19] bundled in the TPP [20]. The mzML files were searched using the pro- tein set described above to which a shuffled decoy set had been appended. The sequences are shuffled by scrambling all amino acids between fixed tryptic cleavage sites. The data were searched with X!Tandem [21] with the K-score plugin [22]. X!Tandem output was processed with the TPP versions of PeptideProphet [23], iProphet (Shteynberg D, Deutsch EW, Lam H, Eng J, Sun Z, Tas- man N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI: iProphet: improved statistical validation of peptide identifications in shotgun proteomics, submitted), and ProteinProphet [24] to extract the maximal identifica- tions with highest confidence scores. All identifications were filtered at a peptide-spectrum-match (PSM) FDR threshold of 0.0001, which yielded a peptide-level FDR of 0.0018 and protein-level FDR of 0.015 as estimated using Page 3 of 11 Number of RAW files 6 468 132 122 85 16 9 13 21 39 39 34 12 1 11 4 29 4 22 36 33 33 33 82 7 1 1 1 6 16 8 12 6 3