Bottom-up proteomics: advancements in sample preparation

VA Duong, H Lee - International journal of molecular sciences, 2023 - mdpi.com
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a
powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom …

Proteomic techniques for characterisation of mesenchymal stem cell secretome

HK Skalnikova - Biochimie, 2013 - Elsevier
Mesenchymal stem cells (MSCs) are multipotent cells with a substantial potential in human
regenerative medicine due to their ability to migrate to sites of injury, capability to suppress …

A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie–Wnt signaling axis in the liver

D Inverso, J Shi, KH Lee, M Jakab, S Ben-Moshe… - Developmental cell, 2021 - cell.com
Single-cell transcriptomics (scRNA-seq) has revolutionized the understanding of the spatial
architecture of tissue structure and function. Advancing the" transcript-centric" view of scRNA …

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

P Vlastaridis, P Kyriakidou, A Chaliotis… - …, 2017 - academic.oup.com
Background Phosphorylation is the most frequent post-translational modification made to
proteins and may regulate protein activity as either a molecular digital switch or a rheostat …

Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers

A Kalli, GT Smith, MJ Sweredoski… - Journal of proteome …, 2013 - ACS Publications
Mass-spectrometry-based proteomics has evolved as the preferred method for the analysis
of complex proteomes. Undoubtedly, recent advances in mass spectrometry instrumentation …

Alpha-synuclein post-translational modifications as potential biomarkers for Parkinson disease and other synucleinopathies

AW Schmid, B Fauvet, M Moniatte… - Molecular & Cellular …, 2013 - ASBMB
The development of novel therapies against neurodegenerative disorders requires the
ability to detect their early, presymptomatic manifestations in order to enable treatment …

Widening the bottleneck of phosphoproteomics: evolving strategies for phosphopeptide enrichment

TY Low, MA Mohtar, PY Lee, N Omar… - Mass spectrometry …, 2021 - Wiley Online Library
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many
biological processes. Whereas phosphoproteomics is a scientific discipline that identifies …

A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis

J Urban - Analytica Chimica Acta, 2022 - Elsevier
Phosphorylation is one of the quickest post-translational modifications that controls
downstream signaling pathways regulating processes like cell proliferation, survival, and …

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

B Istace, A Friedrich, L d'Agata, S Faye, E Payen… - …, 2017 - academic.oup.com
Abstract Background: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently
commercialized MinION, a small single-molecule nanopore sequencer, that offers the …

A tutorial review of labeling methods in mass spectrometry-based quantitative proteomics

Z Wang, PK Liu, L Li - ACS Measurement Science Au, 2024 - ACS Publications
Recent advancements in mass spectrometry (MS) have revolutionized quantitative
proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing …