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MaxQuant is a platform for mass spectrometry-based proteomics data analysis. It includes a peptide database search engine, called Andromeda, and expanding capability to handle data from most quantitative proteomics experiments.
This protocol describes the production of Candida biofilms on the surface of polystyrene roller bottles and subsequent isolation of the biofilm extracellular matrix on a much larger scale than has previously been achieved.
Investigating the ramifications of site-specific protein redox modification in cells is challenging. This protocol uses HaloTagged proteins and a HaloTag-targetable photocaged 4-hydroxynonenal to elicit target-specific modifications and to trace their effects.
The Burgess laboratory describes their functional genomics pipeline based on CRISPR/Cas9-targeted mutagenesis in zebrafish. The system is scalable, enabling phenotypic screening of hundreds of targeted mutants.
Martin et al. describe a protocol to use laser microdissection to isolate specific cells or tissues from tomato fruit. This can be used to perform cell type–specific transcriptome studies in fleshy fruits, as well as in other plant tissues.
This protocol describes how to prepare and use a microfluidic device for measuring chemosensory neuronal activity in Drosophila. The device is reusable and suitable for assessing neurons in larvae, the adult proboscis and the adult leg.
Garcia et al. describe a protocol for mapping-by-sequencing in Tomato. After selecting EMS mutants displaying a phenotype of interest, mutants are back-crossed and causal mutations are identified in the F2 population using sequencing-based approaches.
Primed conversion of photoconvertible fluorescent proteins enables targeted labeling in vivo with high axial resolution. This Protocol describes how to modify a confocal microscope to perform confined primed conversion of Dendra2 in living organisms.
White et al. present a protocol for ARQiv-HTS, a high-throughput reporter-based screening platform that can be used to examine the effects of chemical compound libraries on zebrafish in vivo.
This protocol from Rodrigues et al. describes a cell-free in vitro system to examine the machinery that mediates peroxisomal protein import. The system allows the user to block components of the machinery at virtually any step.
This protocol describes a nondestructive FRET-based assay for measuring protein interactions in cultured cells. The correlation between FRET efficiencies and relative protein concentration can be used to determine relative binding affinities.
Comprehensive analysis of membrane protein interactions using COPIT includes information for transient and weak interactions. This mass spectrometry–based method has optimized steps for removing contaminants and a tailored data analysis.
Fang et al. describe a computational protocol to accurately call indels from whole-genome and whole-exome sequencing data using Scalpel. Important issues for indel identification, such as short repeat regions and varying sequencing coverage, are discussed.