Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras

G Ahn, NM Riley, RA Kamber, S Wisnovsky… - Science, 2023 - science.org
Targeted protein degradation can provide advantages over inhibition approaches in the
development of therapeutic strategies. Lysosome-targeting chimeras (LYTACs) harness …

[HTML][HTML] Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics

AM Scott, C Karlsson, T Mohanty, E Hartman… - Communications …, 2023 - nature.com
Data independent acquisition mass spectrometry (DIA-MS) has recently emerged as an
important method for the identification of blood-based biomarkers. However, the large …

[HTML][HTML] MS-based proteomics of body fluids: the end of the beginning

JM Bader, V Albrecht, M Mann - Molecular & Cellular Proteomics, 2023 - ASBMB
Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet
existing ones are often unspecific and new ones have been very slow to enter the clinic …

Evaluation of DDA Library-Free Strategies for Phosphoproteomics and Ubiquitinomics Data-Independent Acquisition Data

C Wen, X Wu, G Lin, W Yan, G Gan, X Xu… - Journal of Proteome …, 2023 - ACS Publications
Phosphoproteomics and ubiquitinomics data-independent acquisition (DIA) mass
spectrometry (MS) data is typically analyzed by using a data-dependent acquisition (DDA) …

QuantUMS: uncertainty minimisation enables confident quantification in proteomics

F Kistner, JL Grossmann, LR Sinn, V Demichev - BioRxiv, 2023 - biorxiv.org
Mass spectrometry-based proteomics has been rapidly gaining traction as a powerful
analytical method both in basic research and translation. While the problem of error control …

[HTML][HTML] The fitness cost of spurious phosphorylation

D Bradley, A Hogrebe, R Dandage, AK Dubé, M Leutert… - bioRxiv, 2023 - ncbi.nlm.nih.gov
The fidelity of signal transduction requires the binding of regulatory molecules to their
cognate targets. However, the crowded cell interior risks off-target interactions between …

[HTML][HTML] A Cosine-Similarity-Based Deconvolution Method for Analyzing Data-Independent Acquisition Mass Spectrometry Data

X Zhang, R Wu, Z Qu - Applied Sciences, 2023 - mdpi.com
Although data-independent acquisition (DIA) has the ability to identify and quantify all
peptides in a sample, highly complex mixed mass spectra present difficulties for accurate …

[HTML][HTML] Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics

J Wang, W Yu, R D'Anna, A Przybyla, M Wilson… - Molecular & Cellular …, 2023 - ASBMB
Abstract The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium
(CPTAC) provides unique opportunities for cancer target discovery using protein expression …

Using high throughput technologies to understand heterogeneous drug response

GE Boyle - 2023 - search.proquest.com
Heterogeneity is an inherent quality of biological systems, and is one of the properties that
facilitates adaptation of organisms to new environments and stimuli. However, the scientific …