Advances in data‐independent acquisition mass spectrometry towards comprehensive digital proteome landscape

RB Kitata, JC Yang, YJ Chen - Mass spectrometry reviews, 2023 - Wiley Online Library
The data‐independent acquisition mass spectrometry (DIA‐MS) has rapidly evolved as a
powerful alternative for highly reproducible proteome profiling with a unique strength of …

Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023

R Lou, W Shui - Molecular & Cellular Proteomics, 2024 - ASBMB
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …

Sorbitol is a severity biomarker for PMM2‐CDG with therapeutic implications

AN Ligezka, S Radenkovic, M Saraswat… - Annals of …, 2021 - Wiley Online Library
Objective Epalrestat, an aldose reductase inhibitor increases phosphomannomutase (PMM)
enzyme activity in a PMM2‐congenital disorders of glycosylation (CDG) worm model …

Towards structure-focused glycoproteomics

A Chernykh, R Kawahara… - Biochemical Society …, 2021 - portlandpress.com
Facilitated by advances in the separation sciences, mass spectrometry and informatics,
glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling …

midiaPASEF maximizes information content in data-independent acquisition proteomics

U Distler, MK Łącki, MP Startek, D Teschner… - BioRxiv, 2023 - biorxiv.org
Data-independent acquisition (DIA) approaches provide comprehensive records of all
detectable pre-cursor and fragment ions. Here we introduce midiaPASEF, a novel DIA scan …

AAV-based gene therapy prevents and halts the progression of dilated cardiomyopathy in a mouse model of phosphoglucomutase 1 deficiency (PGM1-CDG)

B Balakrishnan, R Altassan, R Budhraja, W Liou… - Translational …, 2023 - Elsevier
Abstract Phosphoglucomutase 1 (PGM1) deficiency is recognized as the third most common
N-linked congenital disorders of glycosylation (CDG) in humans. Affected individuals …

N‐glycoproteomics reveals distinct glycosylation alterations in NGLY1‐deficient patient‐derived dermal fibroblasts

R Budhraja, M Saraswat, D De Graef… - Journal of inherited …, 2023 - Wiley Online Library
Congenital disorders of glycosylation are genetic disorders that occur due to defects in
protein and lipid glycosylation pathways. A deficiency of N‐glycanase 1, encoded by the …

Increasing proteome depth while maintaining quantitative precision in short-gradient data-independent acquisition proteomics

J Doellinger, C Blumenscheit… - Journal of Proteome …, 2023 - ACS Publications
The combination of short liquid chromatography (LC) gradients and data-independent
acquisition (DIA) by mass spectrometry (MS) has proven its huge potential for high …

BoxCarmax: a high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples

B Salovska, W Li, Y Di, Y Liu - Analytical chemistry, 2021 - ACS Publications
The data-independent acquisition (DIA) performed in the latest high-resolution, high-speed
mass spectrometers offers a powerful analytical tool for biological investigations. The DIA …

Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography

M Saraswat, K Garapati, DG Mun, A Pandey - Molecular Omics, 2021 - pubs.rsc.org
Several plasma glycoproteins are clinically useful as biomarkers in a variety of diseases.
Although thousands of proteins are present in plasma,> 95% of the plasma proteome by …