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 …

Ultraviolet photodissociation mass spectrometry for analysis of biological molecules

JS Brodbelt, LJ Morrison, I Santos - Chemical reviews, 2019 - ACS Publications
The development of new ion-activation/dissociation methods continues to be one of the most
active areas of mass spectrometry owing to the broad applications of tandem mass …

An introduction to mass spectrometry-based proteomics

SR Shuken - Journal of Proteome Research, 2023 - ACS Publications
Mass spectrometry is unmatched in its versatility for studying practically any aspect of the
proteome. Because the foundations of mass spectrometry-based proteomics are complex …

Proteomic challenges: sample preparation techniques for microgram-quantity protein analysis from biological samples

P Feist, AB Hummon - International journal of molecular sciences, 2015 - mdpi.com
Proteins regulate many cellular functions and analyzing the presence and abundance of
proteins in biological samples are central focuses in proteomics. The discovery and …

SearchGUI: a highly adaptable common interface for proteomics search and de novo engines

H Barsnes, M Vaudel - Journal of proteome research, 2018 - ACS Publications
Mass-spectrometry-based proteomics has become the standard approach for identifying and
quantifying proteins. A vital step consists of analyzing experimentally generated mass …

From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites

T Hautbergue, EL Jamin, L Debrauwer, O Puel… - Natural Product …, 2018 - pubs.rsc.org
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of
the fungus to its environment. Although some of these natural products are promising …

Identification of Novel Microcystins Using High-Resolution MS and MSn with Python Code

D Baliu-Rodriguez, NJ Peraino… - Environmental …, 2022 - ACS Publications
Cyanotoxins called microcystins (MCs) are highly toxic and can be present in drinking water
sources. Determining the structure of MCs is paramount because of its effect on toxicity …

Generation of antioxidative peptides from Atlantic sea cucumber using alcalase versus trypsin: In vitro activity, de novo sequencing, and in silico docking for in vivo …

Y Zhang, S He, É Bonneil, BK Simpson - Food Chemistry, 2020 - Elsevier
A comprehensive evaluation was conducted to compare the generation of antioxidative
peptides produced by alcalase versus trypsin from Atlantic sea cucumber. The in vitro …

Anatomy and evolution of database search engines—a central component of mass spectrometry based proteomic workflows

K Verheggen, H Ræder, FS Berven… - Mass spectrometry …, 2020 - Wiley Online Library
Sequence database search engines are bioinformatics algorithms that identify peptides from
tandem mass spectra using a reference protein sequence database. Two decades of …

Phosphopeptide fragmentation and site localization by mass spectrometry: an update

CM Potel, S Lemeer, AJR Heck - Analytical chemistry, 2018 - ACS Publications
Pioneering work by, among others, the groups of Hunt and Mann at the start of this century
opened up the era of mass spectrometry (MS)-based phosphoproteomics. 1− 3 Through …