We searched the peptide mapping data using the Sequest algorithm (ThermoFisher Scientific) and did not find any modification to lysine residues.
To identify histone H1, H2A and H2B peptides, a database search was performed using the SEQUEST algorithm within the Bioworks Browser (version 3.3; ThermoFisher Scientific).
For peptide identifications, the generated MS/MS spectra were evaluated using the SEQUEST analysis program and/or Mascot.
Raw spectra were analysed by Bioworks Browser 3.3.1 using the Sequest 3.1 search engine against an indexed database containing all predicted tryptic peptides from T. gondii proteins (ToxoDB release 5.1) [ 65].
To identify peptides, data files were generated from the MS/MS scans by Bioworks 3.0 using the SEQUEST algorithm (threshold, 105; minimum group scan 2, Xc >1.0, Thermo Fisher Scientific) and searched against the complete amino acid database derived from the B. pertussis Tohama genome database.
They were searched against databases for protein identification using the Sequest software.
The peak list files generated by the Bioworks software (Applied Biosystems, USA) using the default parameters were searched against databases for protein identification using the Sequest software.
The mass spectrometry data was analyzed and compared using the Sequest software (Bioworks3.31, Thermo) searching the mouse section of the NR-NCBI database.
MS/MS spectra were searched using the Sequest algorithm with serine, threonine, and tyrosine phosphorylation and methionine oxidation as dynamic modifications.
The proteins were identified using the SEQUEST algorithm and Proteome Discoverer (v 1.3, Thermo Scientific).
