Untargeted metabolomics strategies—challenges and emerging directions

AC Schrimpe-Rutledge, SG Codreanu… - Journal of the …, 2016 - ACS Publications
Metabolites are building blocks of cellular function. These species are involved in enzyme-
catalyzed chemical reactions and are essential for cellular function. Upstream biological …

Quality assurance procedures for mass spectrometry untargeted metabolomics. a review

D Dudzik, C Barbas-Bernardos, A García… - … of pharmaceutical and …, 2018 - Elsevier
Untargeted metabolomics, as a global approach, has already proven its great potential and
capabilities for the investigation of health and disease, as well as the wide applicability for …

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

V Demichev, L Szyrwiel, F Yu, GC Teo… - Nature …, 2022 - nature.com
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …

MSBooster: improving peptide identification rates using deep learning-based features

KL Yang, F Yu, GC Teo, K Li, V Demichev… - Nature …, 2023 - nature.com
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …

A comprehensive subcellular atlas of the Toxoplasma proteome via hyperLOPIT provides spatial context for protein functions

K Barylyuk, L Koreny, H Ke, S Butterworth, OM Crook… - Cell host & …, 2020 - cell.com
Apicomplexan parasites cause major human disease and food insecurity. They owe their
considerable success to highly specialized cell compartments and structures. These …

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

BC Collins, CL Hunter, Y Liu, B Schilling… - Nature …, 2017 - nature.com
Quantitative proteomics employing mass spectrometry is an indispensable tool in life
science research. Targeted proteomics has emerged as a powerful approach for …

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

B Bulik-Sullivan, J Busby, CD Palmer, MJ Davis… - Nature …, 2019 - nature.com
Neoantigens, which are expressed on tumor cells, are one of the main targets of an effective
antitumor T-cell response. Cancer immunotherapies to target neoantigens are of growing …

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

A Palmer, P Phapale, I Chernyavsky, R Lavigne… - Nature …, 2017 - nature.com
High-mass-resolution imaging mass spectrometry promises to localize hundreds of
metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is …

Protein analysis by shotgun/bottom-up proteomics

Y Zhang, BR Fonslow, B Shan, MC Baek… - Chemical …, 2013 - ACS Publications
According to Genome Sequencing Project statistics (http://www. ncbi. nlm. nih.
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …

Metabolite discovery through global annotation of untargeted metabolomics data

L Chen, W Lu, L Wang, X **ng, Z Chen, X Teng… - Nature …, 2021 - nature.com
Liquid chromatography–high-resolution mass spectrometry (LC-MS)-based metabolomics
aims to identify and quantify all metabolites, but most LC-MS peaks remain unidentified …