Data‐independent acquisition mass spectrometry‐based proteomics and software tools: a glimpse in 2020

F Zhang, W Ge, G Ruan, X Cai, T Guo - Proteomics, 2020 - Wiley Online Library
This review provides a brief overview of the development of data‐independent acquisition
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …

Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

L Krasny, PH Huang - Molecular omics, 2021 - pubs.rsc.org
Data-independent acquisition mass spectrometry (DIA-MS) is a next generation proteomic
methodology that generates permanent digital proteome maps offering highly reproducible …

[HTML][HTML] Saturation of the mitochondrial NADH shuttles drives aerobic glycolysis in proliferating cells

Y Wang, E Stancliffe, R Fowle-Grider, R Wang, C Wang… - Molecular cell, 2022 - cell.com
Proliferating cells exhibit a metabolic phenotype known as" aerobic glycolysis," which is
characterized by an elevated rate of glucose fermentation to lactate irrespective of oxygen …

[HTML][HTML] Pan-cancer proteomic map of 949 human cell lines

E Gonçalves, RC Poulos, Z Cai, S Barthorpe… - Cancer Cell, 2022 - cell.com
The proteome provides unique insights into disease biology beyond the genome and
transcriptome. A lack of large proteomic datasets has restricted the identification of new …

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 …

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 …

Eukaryotic cell size control and its relation to biosynthesis and senescence

S **e, M Swaffer, JM Skotheim - Annual review of cell and …, 2022 - annualreviews.org
The most fundamental feature of cellular form is size, which sets the scale of all cell
biological processes. Growth, form, and function are all necessarily linked in cell biology, but …

CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics

A Luna, F Elloumi, S Varma, Y Wang… - Nucleic acids …, 2021 - academic.oup.com
Abstract CellMiner Cross-Database (CellMinerCDB, discover. nci. nih. gov/cellminercdb)
allows integration and analysis of molecular and pharmacological data within and across …

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 …

Histone methyltransferase activity affects metabolism in human cells independently of transcriptional regulation

MF Perez, P Sarkies - PLoS biology, 2023 - journals.plos.org
The N-terminal tails of eukaryotic histones are frequently posttranslationally modified. The
role of these modifications in transcriptional regulation is well-documented. However, the …