Mass-spectrometric exploration of proteome structure and function

R Aebersold, M Mann - Nature, 2016 - nature.com
Numerous biological processes are concurrently and coordinately active in every living cell.
Each of them encompasses synthetic, catalytic and regulatory functions that are, almost …

Challenges and emergent solutions for LC‐MS/MS based untargeted metabolomics in diseases

L Cui, H Lu, YH Lee - Mass spectrometry reviews, 2018 - Wiley Online Library
In the past decade, advances in liquid chromatography‐mass spectrometry (LC‐MS) have
revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply …

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 …

Global detection of human variants and isoforms by deep proteome sequencing

P Sinitcyn, AL Richards, RJ Weatheritt… - Nature …, 2023 - nature.com
An average shotgun proteomics experiment detects approximately 10,000 human proteins
from a single sample. However, individual proteins are typically identified by peptide …

[HTML][HTML] What are the 100 most cited fungal genera?

CS Bhunjun, YJ Chen, C Phukhamsakda… - Studies in …, 2024 - ingentaconnect.com
The global diversity of fungi has been estimated between 2 to 11 million species, of which
only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they …

[HTML][HTML] 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 - Elsevier
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 …

De novo peptide sequencing by deep learning

NH Tran, X Zhang, L **n, B Shan, M Li - Proceedings of the National …, 2017 - pnas.org
De novo peptide sequencing from tandem MS data is the key technology in proteomics for
the characterization of proteins, especially for new sequences, such as mAbs. In this study …

The Perseus computational platform for comprehensive analysis of (prote) omics data

S Tyanova, T Temu, P Sinitcyn, A Carlson, MY Hein… - Nature …, 2016 - nature.com
A main bottleneck in proteomics is the downstream biological analysis of highly multivariate
quantitative protein abundance data generated using mass-spectrometry-based analysis …

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 …

Ultrasensitive proteome analysis using paramagnetic bead technology

CS Hughes, S Foehr, DA Garfield… - Molecular systems …, 2014 - embopress.org
In order to obtain a systems‐level understanding of a complex biological system, detailed
proteome information is essential. Despite great progress in proteomics technologies …