Understudied proteins: opportunities and challenges for functional proteomics

G Kustatscher, T Collins, AC Gingras, T Guo… - Nature …, 2022 - nature.com
Most research aiming at understanding the molecular foundations of life and disease has
focused on a limited set of increasingly well-known proteins while the biological functions of …

Artificial intelligence-based multi-omics analysis fuels cancer precision medicine

X He, X Liu, F Zuo, H Shi, J Jing - Seminars in Cancer Biology, 2023 - Elsevier
With biotechnological advancements, innovative omics technologies are constantly
emerging that have enabled researchers to access multi-layer information from the genome …

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 …

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics

WF Zeng, XX Zhou, S Willems, C Ammar… - Nature …, 2022 - nature.com
Abstract Machine learning and in particular deep learning (DL) are increasingly important in
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …

Artificial intelligence for proteomics and biomarker discovery

M Mann, C Kumar, WF Zeng, MT Strauss - Cell systems, 2021 - cell.com
There is an avalanche of biomedical data generation and a parallel expansion in
computational capabilities to analyze and make sense of these data. Starting with genome …

Making single-cell proteomics biologically relevant

FA Rosenberger, M Thielert, M Mann - Nature Methods, 2023 - nature.com
Recent technological advances in mass spectrometry promise to add single-cell proteomics
to the biologist's toolbox. Here we discuss the current status and what is needed for this …

Accurate de novo peptide sequencing using fully convolutional neural networks

K Liu, Y Ye, S Li, H Tang - Nature Communications, 2023 - nature.com
De novo peptide sequencing, which does not rely on a comprehensive target sequence
database, provides us with a way to identify novel peptides from tandem mass spectra …

A genetic engineering strategy for editing near-infrared-II fluorophores

R Tian, X Feng, L Wei, D Dai, Y Ma, H Pan… - Nature …, 2022 - nature.com
The second near-infrared (NIR-II) window is a fundamental modality for deep-tissue in vivo
imaging. However, it is challenging to synthesize NIR-II probes with high quantum yields …

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 …

Trapped ion mobility spectrometry and parallel accumulation–serial fragmentation in proteomics

F Meier, MA Park, M Mann - Molecular & Cellular Proteomics, 2021 - ASBMB
Recent advances in efficiency and ease of implementation have rekindled interest in ion
mobility spectrometry, a technique that separates gas phase ions by their size and shape …