Protocol Update

Native mass spectrometry can be combined with lipidomic experiments to determine the structural and functional lipids of receptor and transporter assemblies. This protocol describes how to use initial native mass spectrometry results to guide experimental design.

Developing optimal nanozymes requires standardized methods for measuring their catalytic activity and reaction kinetics. This protocol integrates enzyme based Michaelis–Menten kinetics with measured physical properties and computational methods.

The controlled positioning and stoichiometry of aptamers on tetrahedral DNA frameworks enables the synthesis of targeted probes for the capture of circulating tumor cells from blood samples.

We provide an updated protocol for image-based profiling with Cell Painting. A detailed procedure, with standardized conditions for the assay, is presented, along with a comprehensive description of parameters to be considered when optimizing the assay.

LiP-MS is an approach based on limited proteolysis that can be used to probe structural changes in proteins. This update highlights recent changes to the method to improve throughput, proteome coverage and data analysis.

PatternLab is a unified computational environment for analyzing shotgun proteomic data. Version 5 provides modules for preparing sequence databases, protein identification, statistical filtering and in-depth result browsing.

Chemicals are used to induce sporadic and inflammation-associated colon tumor growth in mouse models. When combined with p53 deficiency, tumor development is promoted, including the growth of invasive cancers and lymph node metastasis.

Here the authors describe an updated protocol for single-stranded sequencing library preparation suitable for highly degraded DNA from ancient remains or other sources. The procedure can be performed manually or in an automated fashion.

Here the authors provide an update to their 2013 protocol for using the PANTHER classification system, detailing how to analyze genome-wide experimental data with the newest version of PANTHER (v.14.0), with improvements in the areas of data quality, data coverage, statistical algorithms and user experience.

The COBRA toolbox provides quality-controlled reconstruction, modeling, topological analysis, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data.

This protocol update describes silica-based approaches for purification of DNA from ancient bone, tooth and sediment samples. The optimized buffers yield short DNA fragments compatible with high-throughput sequencing library preparation.

This protocol update describes how to generate mouse models of inflammatory bowel diseases and methods for analyzing disease progression.

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 is an update to the SIFT protocol published in 2009, which uses SIFT 4G to provide SIFT scores from the genomes of more than 200 organisms.