Mass spectrometry‐based high‐throughput proteomics and its role in biomedical studies and systems biology

CB Messner, V Demichev, Z Wang, J Hartl… - …, 2023 - Wiley Online Library
There are multiple reasons why the next generation of biological and medical studies
require increasing numbers of samples. Biological systems are dynamic, and the effect of a …

Instrumentation at the leading edge of proteomics

TM Peters-Clarke, JJ Coon, NM Riley - Analytical Chemistry, 2024 - ACS Publications
The proteome, or collection of proteoforms expressed in a biological system, is dynamic and
heterogeneous. As our appreciation for the complexity of the proteome has evolved, so have …

Evaluating the performance of the astral mass analyzer for quantitative proteomics using data-independent acquisition

LR Heil, E Damoc, TN Arrey, A Pashkova… - Journal of proteome …, 2023 - ACS Publications
We evaluate the quantitative performance of the newly released Asymmetric Track Lossless
(Astral) analyzer. Using data-independent acquisition, the Thermo Scientific Orbitrap Astral …

Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome

FA Rosenberger, M Thielert, MT Strauss, L Schweizer… - Nature …, 2023 - nature.com
Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased
method for the characterization of biological heterogeneity. So far, it has been limited to …

Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics

R Lou, Y Cao, S Li, X Lang, Y Li, Y Zhang… - Nature …, 2023 - nature.com
A plethora of software suites and multiple classes of spectral libraries have been developed
to enhance the depth and robustness of data-independent acquisition (DIA) data …

Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel

M Thielert, ECM Itang, C Ammar… - Molecular Systems …, 2023 - embopress.org
Single‐cell proteomics aims to characterize biological function and heterogeneity at the
level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput …

Immobility-associated thromboprotection is conserved across mammalian species from bear to human

M Thienel, JB Müller-Reif, Z Zhang, V Ehreiser, J Huth… - Science, 2023 - science.org
Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary
embolism is a major cause of morbidity and mortality. Short-term immobility-related …

Prediction of brain metastasis development with DNA methylation signatures

JA Zuccato, Y Mamatjan, F Nassiri, A Ajisebutu… - Nature Medicine, 2025 - nature.com
Brain metastases (BMs) are the most common and among the deadliest brain tumors.
Currently, there are no reliable predictors of BM development from primary cancer, which …

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics

GS Biggs, EE Cawood, A Vuorinen… - Nature …, 2025 - nature.com
Identifying pharmacological probes for human proteins represents a key opportunity to
accelerate the discovery of new therapeutics. High-content screening approaches to expand …

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

NM Lancaster, P Sinitcyn, P Forny… - Nature …, 2024 - nature.com
Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles
in myriad cell processes. That said, detecting and quantifying protein phosphorylation has …