Drosophila melanogaster iTRAQ HCD dataset

Quantitative comparation of the tagmata of body and head using iTRAQ based on HCD Fragmentation. The 8-plex iTRAQ Multiplex Buffer Kit (AB SCIEX, Foster City, CA) was used to label different peptide fractions, in which iTRAQ reagents dissolved in isopropyl alcohol. Another internal standard of D.melanogaster body and head mixed with 1:1 (B+H) was also used when doing iTRAQ labeling. Therefore the same amount of B (body), H1 (head), H2 (head), B+H (internal standard) peptide fractions prepared as described above were labeled by equal but different iTRAQ reagents and incubated for 5 h at room temperature. The four different labeled peptide fractions (B:113, H1:114, H2:115, B+H:116 ) were then mixed with 1:1 and dried in a speedvac followed by desalting purification using stage tip. All prepared peptides were further analyzed on an LTQ-Orbitrap Velos hybrid mass spectrometer (Thermo Electron, San Jose, CA) coupled with UPLC (nano Acquity Ultra Performance LC, Waters). For HCD raw files, the profile data was firstly centralized by ReAdW.exe in TPP and then deisotoped and deconvoluted using in-house made scripts to improve the identification rate of spectra. All MGF files were searched using Mascot 2.3 against a Drosophila melanogaster database with 24,043 entries (http://flybase.org/, release 5.4, 24,043 entries). The target-decoy based strategy was used to control the peptide false discovery rate (FDR).