The emerging role of mass spectrometry-based proteomics in drug discovery

F Meissner, J Geddes-McAlister, M Mann… - Nature Reviews Drug …, 2022 - nature.com
Proteins are the main targets of most drugs; however, system-wide methods to monitor
protein activity and function are still underused in drug discovery. Novel biochemical …

Unbiased spatial proteomics with single-cell resolution in tissues

A Mund, AD Brunner, M Mann - Molecular Cell, 2022 - cell.com
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify
the entire complement of proteins in cells or tissues. Here, we review challenges and recent …

Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform

F Yu, GC Teo, AT Kong, K Fröhlich, GX Li… - Nature …, 2023 - nature.com
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …

A knowledge graph to interpret clinical proteomics data

A Santos, AR Colaço, AB Nielsen, L Niu… - Nature …, 2022 - nature.com
Implementing precision medicine hinges on the integration of omics data, such as
proteomics, into the clinical decision-making process, but the quantity and diversity of …

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

AD Brunner, M Thielert, C Vasilopoulou… - Molecular systems …, 2022 - embopress.org
Single‐cell technologies are revolutionizing biology but are today mainly limited to imaging
and deep sequencing. However, proteins are the main drivers of cellular function and in …

Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition

V Petrosius, P Aragon-Fernandez, N Üresin… - Nature …, 2023 - nature.com
Single-cell resolution analysis of complex biological tissues is fundamental to capture cell-
state heterogeneity and distinct cellular signaling patterns that remain obscured with …

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics

RG Huffman, A Leduc, C Wichmann, M Di Gioia… - Nature …, 2023 - nature.com
Major aims of single-cell proteomics include increasing the consistency, sensitivity and
depth of protein quantification, especially for proteins and modifications of biological interest …

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

V Demichev, CB Messner, SI Vernardis, KS Lilley… - Nature …, 2020 - nature.com
We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural
networks and new quantification and signal correction strategies for the processing of data …

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

ST Gebreyesus, AA Siyal, RB Kitata, ESW Chen… - Nature …, 2022 - nature.com
Single-cell proteomics can reveal cellular phenotypic heterogeneity and cell-specific
functional networks underlying biological processes. Here, we present a streamlined …

Senescent cells promote tissue NAD+ decline during ageing via the activation of CD38+ macrophages

AJ Covarrubias, A Kale, R Perrone… - Nature …, 2020 - nature.com
Declining tissue nicotinamide adenine dinucleotide (NAD) levels are linked to ageing and its
associated diseases. However, the mechanism for this decline is unclear. Here, we show …