Gps explorer software 3

Combined peptide mass fingerprinting PMF and MS/MS queries were performed using the MASCOT search engine 2.2 (Matrix Science, Boston, MA, USA) embedded into GPS-Explorer Software 3.6 (Applied Biosystems, Forster City, CA, USA) on the Swiss Uniport database and NCBI database with the following parameter settings: 100 ppm mass accuracy, trypsin cleavage, one missed cleavage allowed, carbamidomethylation set as fixed modification, oxidation of methionine was allowed as variable modification, and MS/MS fragment tolerance was set to 0.4 Da.

MS and MS/MS data for protein identification were obtained by using a MALDI-TOF-TOF instrument (4700 proteomics analyzer; Applied Biosystems, Foster City, CA). The MS spectra were recorded in reflector mode in a mass range from 800 to 4,000 with a focus mass of 2,000. The TOF/TOF calibration mixtures (AB SCIEX) were used to calibrate the spectrum to a mass tolerance within 10 ppm. For MS calibration, autolysis peaks of trypsin ([M + H] + 842.5100 and 2,211.1046) were used as internal calibrates, and the most intense ion signals (up to 10) were selected as precursors for MS/MS acquisition, excluding the trypsin autolysis peaks and the matrix ion signals.
Peptide mass finger printing PMF and MS/MS queries were performed by using the MASCOT search engine 2.2 (Matrix Science, London, UK) embedded into GPS-Explorer Software 3.6 (Applied Biosystems). A GPS Explorer protein confidence index ≥95% were used to align with the deduced protein sequence of TlXyn11B.

Mass spectrometry and MS/MS data for the recognition of proteins were generated with a MALDI-TOF appliance (4800 plus proteomics analyzer, Applied Biosystems) as described previously [24 (link)]. Collective peptide mass fingerprinting (PMF) and MS/MS inquiries were accomplished by the MASCOT search engine 2.2 (Matrix Science, Ltd., U.S.) fixed into GPS-Explorer Software 3.6 (Applied Biosystems) on NCBI database (Taxonomy: NCBI_Bacteria, number of sequences 32052081, 30/8/2013, NCBI_Mycoplasma, number of sequences 198866, 22/5/2014) and Uniprot database (Number of sequences 540732, 3/9/2013). The identified proteins sequences were obtained from NCBI. Upon comparison to cluster of orthologues groups (COGs) database using RPS-BLAST, functional classification of proteins was determined, and subcellular localization of identified proteins was anticipated with PSORTb database.