Computational protocol: Triethylene Glycol Up-Regulates Virulence-Associated Genes and Proteins in Streptococcus mutans

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Protocol publication

[…] Peptide separation and mass spectrometric analyses were carried out as described previously []. The MS/MS spectra were analysed against the streptococcal protein database (Swiss Prot and TrEMBL, Swiss Institute of Bioinformatics, Geneva, Switzerland, http://ca.expasy.org/sprot/) using SEQUEST algorithm in Proteome Discoverer 1.3 software (Thermo Scientific, San Jose, CA, USA) [].For quantitative proteome analysis, three MS raw files from each group (control and experimental groups) were analyzed using SIEVE software (Version 2.0 Thermo Scientific, San Jose, CA, USA). For the alignment step, a single MS raw file belonging to the control group (no TEG) was selected as the reference file and all of the other files were adjusted to generate the best correlation to this reference file. After alignment, the feature detection and integration (or framing) process was performed using the MS level data. For statistical analyses of protein abundance, peak integrations were summarized into protein-level annotation in SIEVE using a weighted average of intensities for the LC-ESIMS/MS for each protein. In addition, a statistical model based on an ANOVA framework with Tukey’s post hoc test was carried out. All study groups were run 3 separate times to increase coverage of the samples and identify more proteins, with 4 independent samples (using 4 independent S. mutans cultures) in each group. Relative abundance of an individual protein from different TEG concentration groups was considered significantly different from the control group (no TEG) when the values observed were < 0.5 for decreased abundance and >1.5 for increased abundance with a P-value cut-off of < 0.05 [, ]. […]

Pipeline specifications

Software tools Comet, Proteome Discoverer
Databases UniProt ExPASy
Application MS-based untargeted proteomics
Organisms Streptococcus mutans, Streptococcus mutans UA159
Diseases Immunologic Deficiency Syndromes