Mass spectrometry-based proteomics data of Streptococcal Triton X-114

This dataset contains raw and processed mass spectrometry data from six bacterial treated with Triton X-114 extracts. The samples include wild-type and Δlgt mutant strains of Streptococcus gordonii, Streptococcus mutans, and Staphylococcus aureus. Sample Information 1. S. gordonii WT 2. S. gordonii Δlgt 3. S. mutans WT 4. S. mutans Δlgt 5. S. aureus WT 6. S. aureus Δlgt Streptococcal Triton X-114 extracts (3 μg) were separated by SDS-polyacrylamide gel electrophoresis (PAGE) using a 12% gel. After electrophoresis, the gel was stained with Coomassie Brilliant Blue at room temperature for 1 h. Individual lanes were excised and subjected to in-gel digestion using trypsin. The resulting peptides were ionized via electrospray ionization and analyzed using an Orbitrap Exploris 240 mass spectrometer (Thermo Fisher Scientific, MA, USA). Data Analysis Pipeline 1. Raw Data Acquisition - Instrument: Orbitrap Exploris 240, Thermo Fisher Scientific The maximum mass resolution was R = 240,000 with a 1 Hz scan, and the mass accuracy was less than 5 ppm root mean square error with external calibration. 2. File Conversion - RAW → MGF using ProteoWizard MSConvert 3. Peak Detection & Alignment - Software: MASCOT 2.7 - Parameters: threshold of 0.05, two missed trypsin cleavages, and consideration of fixed carbamidomethyl cysteine modification 4. Normalization & Annotation - False discovery rate (FDR): 0.1 - At least 2 unique peptides per protein 6. Output Files - `raw_data/`: mzML files - `processed_data/`: peak tables (.csv), annotation files