The holistic nature of omics studies makes them ideally suited to generate hypotheses on health and disease. Sequencing-based genomics and mass spectrometry (MS)-based proteomics are linked through epigenetic regulation mechanisms. However, epigenomics is currently focused on DNA methylation status using sequencing technologies, while studying histone posttranslational modifications (hPTMs) using MS is lagging, in part because reuse of raw data is impractical. Yet, it is established that targeting these hPTMs using epidrugs is a promising research avenue in cancer treatment. Therefore, we present the most comprehensive MS-based preprocessed hPTM atlas to date, including 21 T-cell acute lymphoblastic leukemia cell lines. We present the data in an intuitive and browsable single licensed Progenesis QIP project and provide all essential quality metrics, allowing users to assess the quality of the data, edit individual peptides, try novel annotation algorithms and export both peptide and protein data for downstream analyses, exemplified by the PeptidoformVisualization tool. This dataset sets the stage for generalizing MS-based histone analysis and provides the first reusable histone dataset for epidrug development.

Propionylated histone peptides were resuspended in 0.1% FA (Biosolve) and spiked with a mixture of beta-galactosidase (SCIEX) and MPDS II (Waters Corporation). 2 µg histone peptides were analysed using the Eksigent NanoLC 425 system operating in capillary flow mode (5µL/min), and coupled to a TripleTOF 6600+ mass spectrometer (SCIEX, Concord, Canada). The samples were loaded at 10µL/min with mobile phase A (0.1% FA in water) and trapped on a TriArt C18 guard column (YMC) (id 500µm, length 5mm, particle size 3 µm) for 3 minutes. Peptides were separated using a 60min reversed-phase gradient on a Phenomenex Luna Omega Polar C18 column (150 x 0.3 mm, particle size 3 µm) at 30°C and at a flow rate of 5µL/min. The following gradient was applied: 3-45% mobile phase B (0.1% FA in ACN), followed by a washing step at 80% B for 15 minutes. The sample list was randomized using a full factorial design and interspersed with QC injections. Each cycle of 2.3s consisted of one MS1 scan (m/z 350-1250) of 250ms, followed by MS2 data-dependent trigger events (m/z 100-1500, high sensitivity mode) of 200ms each. A maximum of 10 candidate precursor ions (charge state 2+ to 5+) exceeding 300 cps were monitored per cycle and these were then dynamically excluded for 10s. Ion source parameters were set to 4.5 kV for the ion spray voltage, 25 psi for the curtain gas, 10 psi for nebulizer gas (ion source gas 1), 20 psi for heater gas (ion source gas 2) and 100°C as source temperature.

6 biological replicates of 21 T-ALL cell lines, namely HSB-2, JURKAT, LOUCY, MOLT-16, RPMI-8402, DND-41, KOPT-K1, PER-117, PF-382, SUP-T11, ALL-SIL, HPB-ALL, PEER, TALL-1, CCRF-CEM, CUTTL1, KARPAS 45, MOLT-4, KE-37, P12-ICHIKAWA) were collected 24 hours after medium was refreshed. After direct acid extraction, histones were propionylated and digested using trypsin.