Ion mobility mass spectrometry (IM-MS) for structural biology: insights gained by measuring mass, charge, and collision cross section

E Christofi, P Barran - Chemical Reviews, 2023 - ACS Publications
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-
MS) techniques has provided substantial insights into the field of structural biology over the …

Navigating the pitfalls of applying machine learning in genomics

S Whalen, J Schreiber, WS Noble… - Nature Reviews Genetics, 2022 - nature.com
The scale of genetic, epigenomic, transcriptomic, cheminformatic and proteomic data
available today, coupled with easy-to-use machine learning (ML) toolkits, has propelled the …

Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

UH Guzman, A Martinez-Val, Z Ye, E Damoc… - Nature …, 2024 - nature.com
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes
in a fast and reproducible manner. Here we present the narrow-window data-independent …

A critical review of bottom-up proteomics: the good, the bad, and the future of this field

EJ Dupree, M Jayathirtha, H Yorkey, M Mihasan… - Proteomes, 2020 - mdpi.com
Proteomics is the field of study that includes the analysis of proteins, from either a basic
science prospective or a clinical one. Proteins can be investigated for their abundance …

Systems biology and multi-omics integration: viewpoints from the metabolomics research community

FR Pinu, DJ Beale, AM Paten, K Kouremenos… - Metabolites, 2019 - mdpi.com
The use of multiple omics techniques (ie, genomics, transcriptomics, proteomics, and
metabolomics) is becoming increasingly popular in all facets of life science. Omics …

The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment

H Rodriguez, JC Zenklusen, LM Staudt, JH Doroshow… - Cell, 2021 - cell.com
When it comes to precision oncology, proteogenomics may provide better prospects to the
clinical characterization of tumors, help make a more accurate diagnosis of cancer, and …

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 …

Optimization of experimental parameters in data-independent mass spectrometry significantly increases depth and reproducibility of results

R Bruderer, OM Bernhardt, T Gandhi, Y Xuan… - Molecular & Cellular …, 2017 - ASBMB
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key
objectives of quantitative proteomics. Here, we present an implementation of data …

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 …

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver …

R Bruderer, OM Bernhardt, T Gandhi… - Molecular & Cellular …, 2015 - ASBMB
The data-independent acquisition (DIA) approach has recently been introduced as a novel
mass spectrometric method that promises to combine the high content aspect of shotgun …