Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

C Ludwig, L Gillet, G Rosenberger, S Amon… - Molecular systems …, 2018 - embopress.org
Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …

The Warburg effect 97 years after its discovery

RM Pascale, DF Calvisi, MM Simile, CF Feo, F Feo - Cancers, 2020 - mdpi.com
Simple Summary The deregulation of the oxidative metabolism in cancer cells,
characterized by an increased ratio between glycolysis and oxygen consumption (Warburgv …

Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders

Y Johmura, T Yamanaka, S Omori, TW Wang… - Science, 2021 - science.org
Removal of senescent cells (senolysis) has been proposed to be beneficial for improving
age-associated pathologies, but the molecular pathways for such senolytic activity have not …

A shift in glutamine nitrogen metabolism contributes to the malignant progression of cancer

M Kodama, K Oshikawa, H Shimizu, S Yoshioka… - Nature …, 2020 - nature.com
Glucose metabolism is remodeled in cancer, but the global pattern of cancer-specific
metabolic changes remains unclear. Here we show, using the comprehensive measurement …

Development of a widely targeted volatilomics method for profiling volatilomes in plants

H Yuan, G Cao, X Hou, M Huang, P Du, T Tan, Y Zhang… - Molecular plant, 2022 - cell.com
Volatile organic compounds play essential roles in plant environment interactions as well as
determining the fragrance of plants. Although gas chromatography-mass spectrometry …

Building ProteomeTools based on a complete synthetic human proteome

DP Zolg, M Wilhelm, K Schnatbaum, J Zerweck… - Nature …, 2017 - nature.com
We describe ProteomeTools, a project building molecular and digital tools from the human
proteome to facilitate biomedical research. Here we report the generation and multimodal …

PKM1 confers metabolic advantages and promotes cell-autonomous tumor cell growth

M Morita, T Sato, M Nomura, Y Sakamoto, Y Inoue… - Cancer cell, 2018 - cell.com
Expression of PKM2, which diverts glucose-derived carbon from catabolic to biosynthetic
pathways, is a hallmark of cancer. However, PKM2 function in tumorigenesis remains …

XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules

X Domingo-Almenara, JR Montenegro-Burke… - Nature …, 2018 - nature.com
We report XCMS-MRM and METLIN-MRM (http://xcmsonline-mrm. scripps. edu/and
http://metlin. scripps. edu/), a cloud-based data-analysis platform and a public multiple …

Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results

C Fernández-Costa, S Martínez-Bartolomé… - Journal of proteome …, 2020 - ACS Publications
Data-independent acquisition (DIA) is a promising technique for the proteomic analysis of
complex protein samples. A number of studies have claimed that DIA experiments are more …

Application of targeted mass spectrometry in bottom-up proteomics for systems biology research

NP Manes, A Nita-Lazar - Journal of proteomics, 2018 - Elsevier
The enormous diversity of proteoforms produces tremendous complexity within cellular
proteomes, facilitates intricate networks of molecular interactions, and constitutes a …