Volume 20 Issue 11, November 2025

Nanoparticle pharmacokinetics is affected by the formation of a protein corona in vivo. Mass spectrometry-based proteomics is essential for understanding the corona composition. This Perspective discusses how method reproducibility can be improved.

Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors from long-read sequencing through the use of long unique molecular identifiers and a high number of polymerase chain reaction duplicates.

Using human induced pluripotent stem cell-derived cardiomyocytes in an organ-on-a-chip model to assay cardiac function: electrophysiology, calcium and contractility. This protocol aims to provide key information on how to reduce variability.

High-throughput computation based on density functional theory (DFT) serves as a cornerstone in materials science. This protocol introduces VASPKIT, a toolkit designed to streamline workflows for the DFT code, Vienna Ab initio Simulation Package.

We provide two procedures to cover distinct approaches for the initiation of lymph node metastases in mice: one for studying the metastatic cascade in tumorigenic cells and the other for studying the effect of metastatic formations in the host.

This is a protocol for the synthesis of ultrasound-sensitive probes that emit sonoafterglow with bright near-infrared emission that are suitable for the deep-tissue imaging of peroxynitrite, a biomarker for M1 macrophages and proinflammatory microenvironments.

Bacterial single-cell sequencing via MATQ-seq combines index sorting, random priming and rRNA depletion, and offers high cell retention and transcript capture rates, making it ideal for experiments with limited starting material.

Studying the role of protein ubiquitination requires well-characterized ubiquitinated protein derivatives. This protocol describes a semisynthetic approach that can be used to make probes for reader proteins, deubiquitinases and ubiquitin carriers.

The Chemical Checker is a collection of small-molecule bioactivity signatures organized in increasing levels of biological complexity. This protocol describes how to incorporate new data, create novel bioactivity spaces and interpret the results.

Engineering enzymes capable of performing chemical transformations requires high-throughput assays to screen activity. In this protocol, reactions in cell lysates are analyzed directly by desorption electrospray ionization (DESI) mass spectrometry.

This Protocol describes optimized procedures for purification and sequencing of small noncoding RNAs from a variety of samples to characterize these diverse RNA species and map them to the parental RNAs from which they originate.

Methods to use polyisocyanide as a model matrix for 3D cell culture. Polyisocyanide gels closely mimic the physical properties of biogels such as collagen and fibrin and, as fully synthetic materials, benefit from reproducibility and customizability.

This Protocol outlines the steps to reconstructing ancient food webs using a variety of fossil data and applying the cascading extinction on graphs model to infer the effects of disturbances on secondary extinction events on the community.