ProteomeXchange dataset

<p>The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD067259 and 10.6019/PXD067259.</p> <div><strong>Sample Processing Protocol</strong></div> <div> <div> <p>Each sample, containing 80 µl of hemolymph and 80 µl of buffer, was centrifuged at 0.5G and 4°C for 5 minutes, after which the plasma was removed using a filter pipette tip. The pelleted hemocytes were washed at least once with EDTA-DPBS or EDTA-ABC buffer using a 5-minute centrifugation step at 0.5G and 4°C. The final hemocyte pellet was resuspended in 15 µl EDTA- DPBS buffer or EDTA-ABC buffer. Subsequently, the samples were digested with 1 µg (1 µg/µl) trypsin (Pierce Thermo Scientific) and incubated at 37°C for one hour. Following incubation, the samples were centrifuged for 5 minutes at 0.5G and 4°C and the supernatants containing the surface determinants were collected. An additional 16-hour peptide digestion was conducted at 37°C using 1 µg (1 µg/µl) of trypsin, after which the samples were stored at -20°C until LC-MS/MS analysis. Peptides were enriched using Agilent Omix Tips according to the manufacturer’s instructions. Peptides were reconstituted in loading solvent A (0.1% TFA in water/ACN (98:2, v/v)). Approximately 2 µg of each sample was subjected to LC-MS/MS analysis using an Ultimate 3000 RSLC nano system with ProFlow Technology (Thermo scientific) linked to an Orbitrap Exploris mass spectrometer (Thermo Scientific) equipped with a Nanospray Flex Ion source (Thermo Scientific).</p> <p>For data analysis, MaxQuant v2.4.4.0 was used together with the A. mellifera (Taxon ID: 7460) database from Uniprot (consulted on 18/09/2023). Trypsin was designated as the digestion enzyme, allowing for a maximum of two missed cleavages and using default identification parameters. Carbamidomethylation of cysteine was set as a fixed modification, while acetylation of N-termini, oxidation of methionine and deamidation of asparagine and glutamine were considered as variable modifications. The false discovery rate (FDR) was set at 1%.</p> <p> </p> <p>This work was supported by the Better-B project, which has received funding from the European Union, the Swiss State Secretariat for Education, Research and Innovation (SERI) and UK Research and Innovation (UKRI) under the UK government's Horizon Europe funding guarantee (grant number 10068544).</p> </div> </div>