LC-MS: Sticking together: Inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling

Experiment Design: growth_condition_design, co-expression_design Experimental Factor: Compound, Organism, Strain Experimental Factor Type: compound, organism, strain_or_line Quality Control Type: technical_replicate, biological_replicate

Specimen Material Type Organism Strain or Line Organism Part Organism Status Sex Age Age Time Unit Sampling Time Point Sampling Time Point Unit Temperature Temperature Unit pH Atmosphere Compound Media Nutrients Fold Change Assignment Name Fold Change Assignment Feature acidiphilium_acidithrix_sup_2 whole_organism Acidiphilium C61 whole culture fresh n/a n/a n/a Acidithrix supernatant acidiphilium_acidithrix_sup_1 whole_organism Acidiphilium C61 whole culture fresh n/a n/a n/a Acidithrix supernatant acidithrix_acidiphilium_sup_1 whole_organism Acidithrix C25 whole culture fresh n/a n/a n/a Acidiphilium supernatant acidithrix_acidithrix_sup_1 whole_organism Acidithrix C25 whole culture fresh n/a n/a n/a Acidithrix supernatant acidiphilium_acidiphilium_sup_2 whole_organism Acidiphilium C61 whole culture fresh n/a n/a n/a Acidiphilium supernatant acidithrix_acidiphilium_sup_2 whole_organism Acidithrix C25 whole culture fresh n/a n/a n/a Acidiphilium supernatant acidithrix_acidithrix_sup_2 whole_organism Acidithrix C25 whole culture fresh n/a n/a n/a Acidithrix supernatant acidiphilium_acidiphilium_sup_1 whole_organism Acidiphilium C61 whole culture fresh n/a n/a n/a Acidiphilium supernatant

Specimen Extract Name Sequence of working steps Protein Amount Amount Unit Volume Volume Unit Label acidiphilium_acidithrix_sup_1 acidiphilium_acidithrix_sup_1_e n/a n/a acidiphilium_acidithrix_sup_2 acidiphilium_acidithrix_sup_2_e n/a n/a acidiphilium_acidiphilium_sup_1 acidiphilium_acidiphilium_sup_1_e n/a n/a acidiphilium_acidiphilium_sup_2 acidiphilium_acidiphilium_sup_2_e n/a n/a acidithrix_acidithrix_sup_1 acidithrix_acidithrix_sup_1_e n/a n/a acidithrix_acidithrix_sup_2 acidithrix_acidithrix_sup_2_e n/a n/a acidithrix_acidiphilium_sup_1 acidithrix_acidiphilium_sup_1_e n/a n/a acidithrix_acidiphilium_sup_2 acidithrix_acidiphilium_sup_2_e n/a n/a

LC-MS/MS Specimen Assay Name LC Instruments LC Peptide Separation Setup LC Stationary Phase Column LC Stationary Phase Temperature LC Temperature Unit LC Mobile Phase Elution ESI Instrument ESI Emitter Type ESI Spray Voltage ESI Voltage Unit ESI Capillary Temperature ESI Temperature Unit ESI S-Lens RF Level MS Mass Detector Type MS Mass Analyser Type MS External Calibration MS Internal Calibration MS Operation Mode MS Mass Range MS Resolution MS Maximum Injection Time MS Time Unit MS Autogain Control Target MS Further Fragmentation Isolisation Width MS Further Fragmentation Collision Energy MS Energy Unit MS Furhter Fragmentation Gas MS2 Mass Range MS2 Resolution MS2 Maximum Injection Time MS2 Time Unit MS2 Autogain Control Target acidithrix_acidiphilium_sup_2 acidithrix_acidiphilium_sup_2_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a acidithrix_acidiphilium_sup_1 acidithrix_acidiphilium_sup_1_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a acidithrix_acidithrix_sup_2 acidithrix_acidithrix_sup_2_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a acidithrix_acidithrix_sup_1 acidithrix_acidithrix_sup_1_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a acidiphilium_acidiphilium_sup_2 acidiphilium_acidiphilium_sup_2_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a acidiphilium_acidiphilium_sup_1 acidiphilium_acidiphilium_sup_1_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a acidiphilium_acidithrix_sup_2 acidiphilium_acidithrix_sup_2_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a acidiphilium_acidithrix_sup_1 acidiphilium_acidithrix_sup_1_lc UltiMate HPG-3400 S (Thermo Fisher Scientific); WPS-3000 Autosampler (Thermo Fisher Scientific) Kinetex C18 RP 50mm × 2.1 mm x 1.7µm 25 degrees_C 3.3 kV 360 degrees_C 50 hybrid quadrupole-orbitrap n/a 50000 n/a n/a

Protocol Name Software Name TANDEM MASS SPECTROMETRY (LC) TraceFinder EFS