Article
Chemistry, Applied
Haixia Zhang, Devini De Silva, Dilanganie Dissanayaka, Thomas D. Warkentin, Albert Vandenberg
Summary: A validated method for separating and quantifying B vitamins from lentil seeds using UHPLC-SRM MS was reported. The study found that the use of three enzymes with a 4-hour incubation was sufficient to convert bound B vitamins into their free forms. A 5-minute UHPLC-SRM MS method was optimized to rapidly analyze 20 B vitamers.
Article
Pharmacology & Pharmacy
Steve Hessmann, Cyrille Chery, Anne-Sophie Sikora, Annick Gervais, Christine Carapito
Summary: Monitoring host cell proteins (HCPs) during monoclonal antibody (mAb) manufacturing is crucial for ensuring the safety and efficacy of drug products. Mass spectrometry (MS) has emerged as an alternative technique for both qualitative and quantitative analysis of HCPs. Liquid chromatography-MS based methods still need to be standardized to provide accurate and sensitive quantification.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2023)
Article
Biochemical Research Methods
Bharath Kumar Raghuraman, Aliona Bogdanova, HongKee Moon, Ignacy Rzagalinski, Eric R. Geertsma, Lena Hersemann, Andrej Shevchenko
Summary: Absolute quantification determines the stoichiometry of proteins in complexes, pathways, or networks by reporting their molar abundance. The use of a generic protein standard called FUGIS allows for quantification of proteins from any organism without the need for isotopic labeling or external calibration. Powered by FUGIS, median-based absolute quantification (MBAQ) outperforms other methods for untargeted proteome-wide quantification.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Kuldeep Giri, Sudipa Maity, Kiran Ambatipudi
Summary: The study identified potential salivary protein markers for metastatic TNBC and successfully differentiated TNBC patients from healthy subjects using targeted proteomics and Western blot analysis.
JOURNAL OF PROTEOMICS
(2022)
Article
Plant Sciences
Andres V. Reyes, Ruben Shrestha, Peter R. Baker, Robert J. Chalkley, Shou-Ling Xu
Summary: Accurate relative quantification is crucial in proteomic studies. Incorporating stable isotope N-15 to plant-expressed proteins in vivo is a powerful tool for accurate quantification, but it faces challenges such as incomplete labeling and contamination. This study demonstrates the use of parallel reaction monitoring (PRM) on a high-resolution mass spectrometer to achieve reliable quantification, even for low abundance proteins.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
David Dierks, Miguel Angel Garcia-Campos, Anna Uzonyi, Modi Safra, Sarit Edelheit, Alice Rossi, Theodora Sideri, Radhika A. Varier, Alexander Brandis, Yonatan Stelzer, Folkert van Werven, Ruth Scherz-Shouval, Schraga Schwartz
Summary: m6A-seq2 is a method that uses multiplexed N-6-methyladenosine immunoprecipitation to compare m6A levels at the site, gene, and sample level, increasing throughput and reducing technical variability and cost. It provides sample-level relative quantitation of m6A and gene-level quantitation, showing that m6A is a main driver of RNA stability in mouse embryonic stem cells.
Article
Biochemical Research Methods
Ignacy Rzagalinski, Aliona Bogdanova, Bharath Kumar Raghuraman, Eric R. Geertsma, Lena Hersemann, Tjalf Ziemssen, Andrej Shevchenko
Summary: The FastCAT method is a fast approach for the absolute quantification of clinically relevant proteins, which improves the accuracy, precision, and dynamic range of quantification without the need for purification of chimeric proteins or the use of gel electrophoresis techniques.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yuxin Zhang, Jie Jiang, Jiongming Ma, Zhen Wei, Yue Wang, Bowen Song, Jia Meng, Guifang Jia, Joao Pedro de Magalhaes, Daniel J. Rigden, Daiyun Hang, Kunqi Chen
Summary: Mapping RNA modifications with advanced technologies has revolutionized our understanding of them. Current modification profiling methods are limited and require selective treatments. Direct RNA sequencing enables the direct study of modifications and has the potential to overcome the limitations of previous methods. The DirectRMDB database provides a fresh perspective on RNA modifications and allows exploration of the epitranscriptome in an isoform-specific manner.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Ziqing Yu, Lei Xu, Weiyuan Lyu, Feng Shen
Summary: Digital biological analysis compartmentalizes targets of interest and performs detection and investigation. This study presents a parallel multistep digital analysis SlipChip, which enables the manipulation of a large number of droplets for digital biological analysis. The SlipChip utilizes a self-partitioning droplet formation mechanism and can perform digital loop-mediated isothermal amplification and digital CRISPR detection in parallel.
Article
Chemistry, Applied
Virginia Prieto-Santiago, Maria del Mar Cavia, Francisco J. Barba, Sara R. Alonso-Torre, Celia Carrillo
Summary: This study developed a highly specific analytical method for the identification and quantification of raffinose family oligosaccharides using liquid chromatography-tandem mass spectrometry. A low-cost and eco-friendly procedure for oligosaccharide extraction from legumes was also proposed, with good precision and repeatability. The method revealed species-related traits for oligosaccharide distribution among 28 different legumes, emphasizing peas as the richest source of prebiotics.
Article
Biochemical Research Methods
Akshada Gajbhiye, Atakan Nalbant, Tiaan Heunis, Frances Sidgwick, Andrew Porter, Yusri Taha, Matthias Trost
Summary: This study developed a rapid and high-throughput method for the detection of SARS-CoV-2 using isotopically labeled synthetic peptides for absolute quantification. The results showed that the method was able to detect positive patients with high viral load in a short time and quantify patients with Ct values as low as 17.8.
JOURNAL OF PROTEOMICS
(2022)
Review
Chemistry, Physical
Malayil Gopalan Sibi, Deepak Verma, Jaehoon Kim
Summary: This review critically discusses catalytic systems for the direct production of aromatics from CO2 via the methanol-mediated and modified Fischer-Tropsch synthesis pathways, covering aspects such as acid sites, catalytic performance, Si/Al ratios of zeolites, proximity between metal oxide and zeolite, and reaction conditions.
CATALYSIS REVIEWS-SCIENCE AND ENGINEERING
(2022)
Article
Chemistry, Physical
Xin-Pu Fu, Peijie Han, Yun-Zhu Wang, Shuai Wang, Ning Yan
Summary: The presence of dissociated ammonia species on Ru nanoparticles enhances its catalytic activity in the dehydrogenation step during amination. In contrast to Pd-based catalysts, the N atom in the generated R-NH2 product binds strongly with Ru sites, inhibiting the formation of undesired secondary amine. This work reveals the overlooked role of ammonia in the amination reaction over Ru-based catalysts.
JOURNAL OF CATALYSIS
(2021)
Article
Energy & Fuels
Ya-Rong Zheng, Jerome Vernieres, Zhenbin Wang, Ke Zhang, Degenhart Hochfilzer, Kevin Krempl, Ting-Wei Liao, Francesco Presel, Thomas Altantzis, Jarmo Fatermans, Soren Bertelsen Scott, Niklas Morch Secher, Choongman Moon, Pei Liu, Sara Bals, Sandra Van Aert, Ang Cao, Megha Anand, Jens K. Norskov, Jakob Kibsgaard, Ib Chorkendorff
Summary: This study presents a low-iridium mass-selected iridium-tantalum oxide catalyst with high intrinsic activity for acid environments, aiming to improve the efficiency of hydrogen production in water electrolysers. By carefully evaluating oxygen production, the researchers demonstrate that the catalyst exhibits higher activity compared to commercial IrO2.
Article
Agriculture, Multidisciplinary
Anna-Lena Kertsch, Juliet Wagner, Thomas Henle
Summary: During beer and wine production, Maillard reaction products(MRPs) are formed, affecting the taste and aroma of the beverages. This study analyzed the amounts of specific compounds (3-DG, 3-DGal, MGO, GO, HMF, and FF) in 36 selected wines using HPLC-UV and GC-MS. 3-DG was found to be the dominant compound, and several yeast metabolites were also detected for the first time. Differences between red and white wines suggested that enological parameters could influence MRP contents.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dominic P. Byrne, Safal Shrestha, Leonard A. Daly, Vanessa Marensi, Krithika Ramakrishnan, Claire E. Eyers, Natarajan Kannan, Patrick A. Eyers
Summary: Pseudokinases lack conserved amino acids for catalytic activity and have diverse biological functions. Human PSKH2 is a pseudokinase closely related to the canonical kinase PSKH1. Species-level adaptations have led to the appearance of PSKH2 variants alongside PSKH1 in vertebrate genomes. PSKH2 lacks protein phosphotransferase activity and its N-terminal domain is required for stable expression and localization to the mitochondrial fraction. PSKH2 is part of a mitochondrial protein network and its expression is regulated through the HSP90/Cdc37 chaperone system.
BIOCHEMICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Martin Rusilowicz, David W. Newman, Declan R. Creamer, James Johnson, Kareena Adair, Victoria M. Harman, Chris M. Grant, Robert J. Beynon, Simon J. Hubbard
Summary: Protein quantitation via mass spectrometry requires the use of peptide proxies, and accurate quantitation often relies on the addition of an external standard. AlacatDesigner is a tool that assists in selecting suitable peptide candidates for recombinant protein standards. It considers factors such as target protein, existing databases, literature occurrence, potential post-translational modifications, and ionization potential within the mass spectrometer.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Medicinal
Ines Ventura, Victoria Harman, Robert J. Beynon, Romana Santos
Summary: Biomedical adhesives still struggle with strong adhesion in wet environments. Marine invertebrates' biological adhesives show promising characteristics for underwater biomimetic adhesives. Through analysis of sea urchin Paracentrotus lividus adhesive proteins, researchers identified glycosylated protein candidates. The deeper characterization of these adhesive glycoproteins advances the development of sea urchin-inspired bioadhesives.
Article
Biochemistry & Molecular Biology
Martin D. Jennings, Priya Srivastava, Christopher J. Kershaw, David Talavera, Christopher M. Grant, Graham D. Pavitt
Summary: Cells respond to oxidative stress by reprogramming gene expression to enhance levels of antioxidant enzymes. In Saccharomyces cerevisiae, proteins Slf1 and Sro9 play a role in protein synthesis adaptation during stress. Slf1 is identified as a ribosome-associated translational modulator that promotes translation of highly-translated mRNAs, facilitating cell survival and adaptation to stress.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jack Llewellyn, Venkatesh Mallikarjun, Ellen Appleton, Maria Osipova, Hamish T. J. Gilbert, Stephen M. Richardson, Simon J. Hubbard, Joe Swift
Summary: Cells respond to stress by producing chaperone proteins to maintain protein function, but aging leads to a disruption of protein balance and the formation of disease-related protein aggregates. Understanding the molecular causes of this proteostasis deterioration is important for disease interventions and cell health maintenance in regenerative medicine strategies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Leandro Xavier Neves, R. Alan Wilson, Philip Brownridge, Stephen W. W. Holman, Victoria M. M. Harman, Claire E. E. Eyers, Robert J. J. Beynon, William Castro-Borges
Summary: In this study, a detailed method for preserving the proteome of adult Schistosoma mansoni worms was described in order to enrich the tissues associated with the parasite's alimentary tract. The methodology employed label-free and QconCAT-based absolute quantification to detect S. mansoni oesophageal gland products. By stabilizing the proteome and minimizing sample degradation during dissection, the hidden proteome of target tissues, which are not readily available from total lysates due to their small volumes, could be accessed. This protocol can be used for the discovery of proteins with potential diagnostic and therapeutic utility in other Schistosoma species lacking quantitative proteomics characterization of specialized tissues.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Jana Schepers, Zorana Carter, Paraskevi Kritsiligkou, Chris M. Grant
Summary: This study reveals that methionine oxidation is a key factor in the formation of the yeast [PSI+] prion. By lacking methionine sulfoxide reductases, it is found that [PSI+] formation is increased, while lacking both isoenzymes of methionine sulfoxide reductases reduces [PSI+] formation.
Article
Biochemistry & Molecular Biology
Joanne Cunningham, Aristeidis P. Sfakianos, Paraskevi Kritsiligkou, Christopher J. Kershaw, Alan J. Whitmarsh, Simon J. Hubbard, Mark P. Ashe, Chris M. Grant
Summary: Translation initiation factor 4G (eIF4G) is crucial for translation initiation. In yeast, eIF4G1 is specifically required for the translational response to oxidative stress.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Jonathan P. Green, Catarina Franco, Amanda J. Davidson, Vicki Lee, Paula Stockley, Robert J. Beynon, Jane L. Hurst
Summary: Breeding females can cooperatively rear their offspring, but this may lead to risks of exploitation. In lactating mammals, communal rearing is more common among close relatives. This study used a dual isotopic tracer approach to track milk allocation in familiar pairs of sisters and unrelated house mice. The results showed that closely related pairs had lower energy demand and the pups had better access to non-maternal milk. However, there was a greater energetic cost for females when rearing offspring with an unrelated partner.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Leonard A. Daly, Dominic P. Byrne, Simon Perkins, Philip J. Brownridge, Euan Mcdonnell, Andrew R. Jones, Patrick A. Eyers, Claire E. Eyers
Summary: In this study, a MS-based workflow for sY-peptide characterization was developed, allowing systematic investigation of the sulfome. The key for distinguishing sulfated peptides from phosphopeptides was low collision energy-induced neutral loss. Applying this workflow identified 21 new sulfotyrosine-containing proteins and revealed new interplay between enzymes relevant to both protein and glycan sulfation.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Allen Po, Claire Eyers
Summary: Top-down proteomics aims to identify and analyze intact proteoforms extracted from biological samples. However, defining and pinpointing post-translational modifications on intact proteins remains a challenge. This is crucial for understanding the specific roles and structure-function relationships of proteins.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Chemistry, Multidisciplinary
Leonard A. Daly, Christopher J. Clarke, Allen Po, Sally O. Oswald, Claire E. Eyers
Summary: The article focuses on the application of mass spectrometry in the identification and quantification of protein modifications, specifically phosphorylation and sulfation. It discusses the challenges associated with discriminating and pinpointing the sites of these modifications on polypeptide chains. The article showcases various approaches for enrichment and site localisation of phosphorylated and sulfated peptides, as well as modification analysis in intact proteins. It also discusses the use of native ion-mobility MS to explore the effects of these modifications on protein structure and ligand binding. The article provides insights into the current strategies and future directions in studying phosphorylation and sulfation using mass spectrometry.
CHEMICAL COMMUNICATIONS
(2023)