Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript.
This protocol integrates genome-wide CRISPR knockout screening of toxins with in silico drug profiling for a new approach to targeted antidote development.
The morphological and molecular preservation of fresh-frozen tissues is difficult. Embedding with an hydroxypropyl methylcellulose/polyvinylpyrrolidone-rich hydrogel results in a material compatible with spatial biochemical analysis (e.g., mass spectrometry imaging), enabling multimodal data integration.
Untargeted mass spectrometry (MS) produces complex, multidimensional data. The MZmine open-source project enables processing of spectral data from various MS platforms, e.g., liquid chromatography–MS, gas chromatography–MS, MS–imaging and ion mobility spectrometry–MS, and is specialized for metabolomics.
This tutorial provides guidelines on oncolytic virus design, production and testing in cancer immunotherapy. Best practice recommendations for preclinical and clinical use of oncolytic viruses as an immunotherapy tool and related future challenges are also considered.
This protocol presents ProBac sequencing, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets.
MSstats is used for the statistical analysis of proteomics data from DIA mass spectrometry experiments. This protocol describes workflows using (i) the MSstatsShiny graphical user interface and (ii) the R packages MSstats or MSstatsBig (for larger datasets).
Springer Nature recently acquired protocols.io, an open-access platform for developing and sharing protocols, which will replace the Protocol Exchange from June 2024.
Community-generated online templates for harmonized data reporting ensure that data and metadata associated with experiments are findable, accessible, interoperable, reusable and compiled for consistency in experimental design and test performance.
This protocol is for using xMarkerFinder, a four-stage computational framework, to enable the identification and validation of reproducible microbial biomarkers from cross-cohort studies, and establish potential microbiome-induced mechanisms.
This protocol presents a metabolomics method tailored for detecting and measuring gut-microbe-derived metabolites using a broad reference library of metabolite standards.
This protocol describes toxin activation–inhibition conjugation (TAC–TIC), a reverse genetics screening approach that can be used to identify triggers or blockers of bacterial toxin–antitoxin or phage immunity systems.
The buildup and operation of a custom single-molecule localization microscope with state-of-the-art performance and advanced features bridges the gap between entry-level open-source projects and costly commercial systems.
This protocol details the generation of cortical organoids with complex neural oscillations through a ‘semi-guided’ protocol, and their functional characterization using microelectrode array measurements, calcium imaging and adeno-associated virus transduction.
Ancient proteins carry genetic information from fossils that are too old or degraded for ancient DNA recovery. This protocol describes the extraction and tandem mass spectrometry sequencing of million-year-old dental enamel proteins for phylogenetic inference.
This protocol details methods for using methanol in methylation reactions, including the synthesis of suitable transition metal-containing catalysts, and in the synthesis of heterocycles. The methods described produce only H2 and H2O as by-products.
Isotope ratio mass spectrometry as described in this protocol can be used to determine natural variation in the abundance of stable isotopes in individual compounds to provide information relevant to metabolism, ecology or climate change.
Surface photovoltage microscopy as described in this protocol allows high spatial and energy resolution mapping of surface-charge distributions on photocatalyst particles, enabling rational design of improved materials.
NanoLuciferase- and HaloTag-based screening technologies are versatile tools suitable for the live-cell analysis of the entire small-molecule-induced degradation cascade to uncover the mode of action of proximity-inducing compounds such as PROTACs.
This protocol describes the preparation of long-lasting aggregation-induced emission-based, near-infrared afterglow luminescence nanoprobes. Their enhanced afterglow intensity results in improved imaging sensitivity and depth in vivo.