Proteomic analysis was conducted to reveal the relative protein abundance levels during the conjugation process. Digested protein (sample preparation in SI Text S8 ) was then analysed by liquid chromatography (Ultimate® 3000 RSLCnano system, Thermo Scientific™)‐tandem mass spectrometry (Q‐Exactive™ H‐X Hybrid Quadrupole‐Orbitrap™ mass spectrometer, Thermo Scientific™) (LC–MS/MS). After protein sequencing, raw data were processed by Thermo Proteome Discoverer (version 2.2.0.388) against the E. coli MG1655 and P. alloputida KT2440 database (Uniport, accessed on 12 July 2019). The abundance ratio of each protein was calculated by dividing the abundance of the drug treated sample by that of the drug‐free control sample. Proteins with false discovery rate (FDR), q value, less than 0.01 were considered to have significant expression differences.
Q exactive h x hybrid quadrupole orbitrap mass spectrometer
Manufactured by Thermo Fisher Scientific
The Q-Exactive™ H-X Hybrid Quadrupole-Orbitrap™ mass spectrometer is a high-resolution, accurate-mass (HRAM) instrument that combines a quadrupole mass filter with an Orbitrap mass analyzer. It provides high-throughput, sensitive, and accurate mass analysis for a variety of applications.
Automatically generated - may contain errors
2 protocols using q exactive h x hybrid quadrupole orbitrap mass spectrometer
1
Proteomic Analysis of Conjugation Process
2
Proteomic Analysis of Enrichment Cultures
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For protein extraction, enrichment cultures collected from Phase 1 and 2 (10 ml each phase) were pelleted by centrifugation (18 000 g, 4°C) and then washed with 1 × Phosphate buffered saline (PBS). The cell lysis and total protein digestion were performed as described previously [16 (link)]. The digested peptides were analysed by liquid chromatography–tandem mass spectrometry using a Dionex Ultimate 3000 RSLCnano-LC system coupled to a Q-Exactive H-X Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Scientific). Mass spectra were searched against the annotated closed MAGs of E and B, respectively, in Thermo Proteome Discoverer. The identified proteins contained at least one unique peptide with a stringency cut-off of false discovery rate (q value) <0.05.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!