All MS/MS spectra from 1D-PAGE-LC-MS/MS experiments were searched against the two protein sequence databases using the SEQUEST (v.27, rev.
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].
The mass spectrometry data were analyzed using the Sequest 3.31 software (J Eng and J Yates, University of Washington, Seattle, WA, USA, and Finnigan, San Jose, CA, USA) and Pep-Miner searching against the human part of the NCBI-NR database.
The mass spectrometry data was clustered and analyzed by using the Sequest software [15] and Pep-Miner [16] searching engine against the Human part of the NR-NCBI database.
Mass spectra were searched against a protein database using the SEQUEST [ 25] algorithm in Bioworks 3.3 (Thermo Fisher Scientific).
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.
The mass spectrometry data was analyzed and compared using the Sequest software (Bioworks3.31, Thermo) searching the mouse section of the NR-NCBI database.
Acquired spectra were searched against the human SwissProt database (091813) using the Sequest search engine through PD1.4 (Thermo-Scientific, Alcobendas, Madrid, Spain).
The MS/MS spectra were searched against the NCBI non-redundant protein sequence database using the SEQUEST computer algorithm [11] to produce a list of proteins identified in each sample.
MS/MS spectra were searched using the Sequest algorithm against Smad1 protein with dynamic modification of methionine oxidation and serine, threonine and tyrosine phosphorylation.
For protein identification, the MS spectra results were searched against the 2 August 2013 release of the C. thermocellum DSM1313 genome available at the NCBI website (NCBI reference sequence NC_017304.1) using the SEQUEST program from the Thermo Discoverer Proteome 1.0 database.
