The DNA adducts were measured by UPLC-ESI/MS3 employing a Dionex Ultimate 3000 LC (Thermo Fisher, San Jose, CA) equipped with a Thermo Acclaim PepMap trap cartridge RP C18 (0.3mm × 5 mm, 5 μm particle size, 100 Å), a Michrom Magic C18 AQ column (0.3 mm×150 mm, 3 μm particle size), and a Michrom Captive Spray source (Auburn, CA) interfaced with a linear ion trap mass spectrometer Velos Pro (Thermo Scientific, San Jose, CA). The chromatography conditions, MS parameters and the MS3 transitions used to monitor the DNA adducts in the positive ionization mode are reported in supporting information (Nauwelaers et al. 2011 (link)). External calibration curves were constructed for quantification (Goodenough et al. 2007 (link)).
Captive spray source
Manufactured by Thermo Fisher Scientific
The Captive Spray source is a type of ion source used in mass spectrometry instrumentation. It is designed to introduce and ionize liquid samples into the mass spectrometer for analysis. The core function of the Captive Spray source is to generate ions from the liquid samples in a controlled and efficient manner, enabling the mass spectrometer to detect and analyze the composition of the samples.
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Lab products found in correlation
Dionex ultimate 3000 lc, by Thermo Fisher Scientific (2 mentions)
Acclaim pepmap trap cartridge rp c18, by Thermo Fisher Scientific (2 mentions)
Magic c18 aq column, by Thermo Fisher Scientific (2 mentions)
Velos pro, by Thermo Fisher Scientific (1 mentions)
Q exactive orbitrap mass spectrometer, by Thermo Fisher Scientific (1 mentions)
Hplc system, by Thermo Fisher Scientific (1 mentions)
Scaffold 3, by Proteome Software (1 mentions)
Speedbead magnetic carboxylate modified particles, by GE Healthcare (1 mentions)
3 protocols using captive spray source
1
Quantification of DNA Adducts by UPLC-MS/MS
2
Proteomics Analysis of Microbial Cultures
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For both strains, 200 mL of each triplicate culture were filtered onto 0.2 μm Supor polyethersulfone filters, and filters were flash frozen in liquid nitrogen and stored until analysis. See Supplementary methods for detailed proteomics analysis steps. Briefly, proteins were extracted using protein extraction buffer (50 mM HEPES pH 8.5, Boston BioProducts) and digested via magnetic beads (SpeedBead Magnetic Carboxylate Modified Particles, GE Healthcare). Tryptic peptides were analyzed via liquid chromatography tandem mass spectrometry (LC/MS/MS) using a Michrom Advance HPLC system with reverse phase chromatography coupled to a Thermo Scientific Q-Exactive Orbitrap mass spectrometer with a Michrom Advance CaptiveSpray source. Scaffold 3 (version 5.1.2, Proteome Software, Inc.) was used to visualize and process the proteomics data, and spectra were converted to normalized total spectral counts (Spectral Counts) (see Supplementary methods ).
3
Quantification of DNA Adducts by UPLC-MS3
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