Review
Biochemical Research Methods
Shuting Xu, Huwei Liu, Yu Bai
Summary: Immunoassay is a crucial clinical technique for disease diagnosis. Mass spectrometry immunoassays (MSIAs) have become popular due to their powerful readout capabilities and improved sensitivity through the development of mass labels. MSIAs have expanded from element-based methods to laser-based and ambient MS, offering high potential for clinical applications such as biomarker screening and single-cell analysis.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Junjie Hu, Fei Liu, Yunlong Chen, Guoqiang Shangguan, Huangxian Ju
Summary: This review summarizes the principle of mass spectrometric sensing, construction of different mass tags for biosensing, and typical combination mode of mass spectrometric imaging (MSI) technique. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to advance the field of mass spectrometric biosensing.
Article
Chemistry, Analytical
Claudia Ctortecka, Karel Stejskal, Gabriela Krssakova, Sasha Mendjan, Karl Mechtler
Summary: Advancements in single-cell proteomics workflows have enhanced sensitivity and reproducibility for characterizing unknown biological phenomena. The introduction of multiplexed single-cell proteomics has led to a trend of combining single-cell measurements with abundant carriers to improve precursor selection and identification accuracy, although extreme carrier spikes may affect quantitative accuracy. Narrowly titrated carrier spikes have been found to provide comparable sensitivity with superior accuracy, while alternative multiplexing strategies can help evaluate data quality. Ultimately, optimized experimental designs for multiplexed proteomics of trace samples can lead to improved quantitative accuracy and elevated replicate overlap.
ANALYTICAL CHEMISTRY
(2022)
Article
Medical Laboratory Technology
Matthijs Vynck, Friedel Nollet, Lode Sibbens, Helena Devos
Summary: This study explores the reasons why preferential observation of alleles may lead to method bias and why this bias requires the exclusion of certain markers. It introduces a bias reduction approach in the data analysis phase, which improves accuracy and precision under all circumstances and allows achievement of an assay's theoretically achievable informativity rate. Additionally, several strategies to reduce biases in the assay design phase are proposed.
CLINICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Andrea Annibal, Roberto Ripa, Eugen Ballhysa, Christian Latza, Nadine Hochhard, Adam Antebi
Summary: Cyclic dinucleotides (CDNs) are critical secondary messenger molecules that trigger cellular signaling cascades. cGAS plays a key role in synthesizing 2'3' cGAMP, which in turn regulates immune function and antiviral responses. The study presents a novel LC-MS/MS method for quantifying CDNs and highlights the importance of parameter optimization for sensitivity and accuracy.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Margaux Fresnais, Siwen Liang, Deniz Seven, Nevena Prodanovic, Julia Sundheimer, Walter E. Haefeli, Juergen Burhenne, Remi Longuespee
Summary: The development and validation of desorption/ionization mass spectrometric assays for drug quantification in tissue sections is crucial for their widespread application in (clinical) pharmacology. Advances in desorption electrospray ionization have demonstrated its usefulness for developing targeted quantification methods that meet validation requirements. Factors such as desorption spot morphology, analytical time, and sample surface need to be considered for successful method development. This study highlights the importance of considering desorption kinetics during DESI analyses, which can help reduce analytical time, verify solvent-based drug extraction methods, and predict feasibility of imaging assays. These findings provide valuable guidance for future development of validated DESI-profiling and imaging methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Engineering, Chemical
Akos Kuki, Gergo Roth, Anna Nagy, Miklos Zsuga, Sandor Keki, Tibor Nagy
Summary: This article introduces a new data mining approach for simplifying copolymer mass spectra and determining their composition. By selecting the most abundant peak in the mass spectrum for calculation, the quantities and properties of the copolymer can be determined more efficiently.
Article
Chemistry, Analytical
Emily R. Groper, Jack A. Barnes, Rory McEwen, Younes Messaddeq, Richard D. Oleschuk, Hans-Peter Loock
Summary: A new method for fabricating a multiplexed electrospray emitter with multiple micronozzles was proposed in this study. By adjusting water flow during wet chemical etching of microstructured silica fibers, micro-axicon lenses were formed along with micronozzles, enhancing mass-spectrometry throughput.
Article
Biochemical Research Methods
Da Kuang, Jochen Weile, Nishka Kishore, Alan F. Rubin, Stanley Fields, Douglas M. Fowler, Frederick P. Roth
Summary: The MAVEs testing method allows for experiments on all possible variants in selected genomic regions, providing important data for rapid and accurate clinical interpretation of human variation. The MaveRegistry platform has been developed to facilitate collaboration, reduce redundant efforts, and track and share progress on ongoing MAVE projects within the rapidly growing international community using MAVE approaches.
Article
Biochemistry & Molecular Biology
Adina Borbely, Lilla Petho, Ildiko Szabo, Mohammed Al-Majidi, Arnold Steckel, Tibor Nagy, Sandor Keki, Gergo Kallo, Eva Csosz, Gabor Mezo, Gitta Schlosser
Summary: The use of peptide-drug conjugates as targeted antitumor therapeutics has gained significant attention. Our study focused on optimizing fragmentation conditions to suppress dissociation of anthracycline drug and provide good sequence coverage in tandem mass spectrometry. We found that electron-based dissociation methods can inhibit peptide backbone fragmentation, while efficient HCD fragmentation is influenced by factors such as amino acid sequences and charge states. High energy HCD and MALDI-TOF/TOF with CID mode are recommended for unambiguous sequence assignment and differentiation of conjugate isomers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Hao Yin, Yanxin Chu, Wei Wang, Zhenzhen Zhang, Zhen Meng, Qianhao Min
Summary: Revealing multiple biomolecules simultaneously in biological and biomedical research is challenging due to their low abundance and poor ionization efficiency. Mass spectrometry (MS) offers unique advantages in multiplexed and label-free analyses, but direct MS profiling of these biomolecules remains difficult. A potential solution to this issue is the use of mass tag (MT)-encoded nanointerfaces, which convert the abundance or activity of biomolecules into amplified ion signals, enabling synchronous MS analysis of multiple targets. This review provides a comprehensive overview of recent advances in MT-encoded nanointerfaces for multiplexed MS bioanalysis and biomedical research, covering their structural characteristics, applications in biomarker assays, cell analysis, and tissue imaging, as well as future prospects.
Article
Biochemical Research Methods
Fumihiko Takeuchi, Norihiro Kato
Summary: The study utilized nonlinear ridge regression for cell-type-specific epigenome-wide association analysis, addressing the issues of scaling and multicollinearity with good performance. The marginal model was able to detect weak signals in real data but had lower precision.
BMC BIOINFORMATICS
(2021)
Article
Chemistry, Medicinal
Zhongqi Zhang, Sih-Yao Chow, Ronandro De Guzman, Nathan H. Joh, Marisa K. Joubert, Jason Richardson, Bhavana Shah, Mats Wikstrom, Zhaohui Sunny Zhou, Jette Wypych
Summary: This study characterizes light-induced modifications on therapeutic proteins through irradiation experiments and identifies a list of potential modifications. The findings provide a database for routine characterization of light-induced modifications on therapeutic proteins.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Petr G. G. Lokhov, Elena E. E. Balashova, Oxana P. P. Trifonova, Dmitry L. L. Maslov, Anatoly I. I. Grigoriev, Elena A. A. Ponomarenko, Alexander I. I. Archakov
Summary: In metabolomics, a mass spectrometric metabogram was developed to simplify and clinically measure the blood plasma metabolome. The metabogram was created using direct infusion mass spectrometry and principal component analysis, and it provides clinically relevant information about blood metabolome variability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Aziz Ur Rehman Safi, Magdi Mansour Salih, Hazir Rahman, Baharullah Khattak, Ahmad El Askary, Eman Hussain Khalifa, Muhammad Qasim
Summary: In this study, an immunoaffinity-based proteomic approach was used to identify 28 immunoreactive proteins of Salmonella Typhi. These proteins have diverse functions related to virulence and pathogenesis, energy metabolism, cell development, biosynthesis of amino acids, regulatory functions, and biosynthesis of cofactors. The findings of this study will contribute to the development of improved vaccines and diagnostic tools for typhoid fever.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2023)
Article
Biochemical Research Methods
Jennifer G. Abelin, Jinal Patel, Xiaodong Lu, Caitlin M. Feeney, Lola Fagbami, Amanda L. Creech, Roger Hu, Daniel Lam, Desiree Davison, Lindsay Pino, Jana W. Qiao, Eric Kuhn, Adam Officer, Jianxue Li, Susan Abbatiello, Aravind Subramanian, Richard Sidman, Evan Snyder, Steven A. Carr, Jacob D. Jaffe
MOLECULAR & CELLULAR PROTEOMICS
(2016)
Article
Chemistry, Analytical
Lindsay K. Pino, Brian C. Searle, Eric L. Huang, William Stafford Noble, Andrew N. Hoofnagle, Michael J. MacCoss
ANALYTICAL CHEMISTRY
(2018)
Article
Biochemical Research Methods
Lindsay Pino, Andy Lin, Wout Bittremieux
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Lindsay K. Pino, Brian C. Searle, Han-Yin Yang, Andrew N. Hoofnagle, William S. Noble, Michael J. MacCoss
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Cell Biology
Alexander J. Federation, Vivek Nandakumar, Brian C. Searle, Andrew Stergachis, Hao Wang, Lindsay K. Pino, Gennifer Merrihew, Ying S. Ting, Nicholas Howard, Tanya Kutyavin, Michael J. MacCoss, John A. Stamatoyannopoulos
Review
Biochemical Research Methods
Lindsay K. Pino, Seth C. Just, Michael J. MacCoss, Brian C. Searle
MOLECULAR & CELLULAR PROTEOMICS
(2020)
Article
Biochemical Research Methods
Lindsay K. Pino, Josue Baeza, Richard Lauman, Birgit Schilling, Benjamin A. Garcia
Summary: The study presents a workflow combining SILAC and DIA-MS using free software, showing that DIA achieves similar peptide detection numbers as DDA but with improved quantitative accuracy and precision for SILAC by an order of magnitude. Application of SILAC-DIA-MS to determine protein turnover rates reveals more sensitive protein turnover models and identifies known proteins degraded by the ubiquitinproteasome pathway, as well as proteins with slower turnover rates implicated in invasive breast cancer. The improved quantification from DIA is expected to make SILAC-based experiments like protein turnover more sensitive.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemical Research Methods
Lindsay Pino, Birgit Schilling
Summary: Novel technologies and workflows have advanced the study of protein dynamics across space and time, providing high precision and throughput. Techniques such as proximity labeling, protein localization, and separation-based methods offer insights into biological complexity, protein networks, and potential therapeutic interventions.
EXPERT REVIEW OF PROTEOMICS
(2021)
Article
Chemistry, Analytical
Richard Lauman, Hee Jong Kim, Lindsay K. Pino, Alessandro Scacchetti, Yixuan Xie, Faith Robison, Simone Sidoli, Roberto Bonasio, Benjamin A. Garcia
Summary: Post-transcriptional modifications greatly affect the structure and function of RNA. Current sequencing and mass spectrometry methods have limitations in accurately identifying and cataloging RNA modifications. We have developed a new approach that combines high-field asymmetric ion mobility separation and electrochemically modulated liquid chromatography, which significantly improves the coverage and throughput of RNA sequencing while allowing for precise identification and localization of RNA modifications.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Carolyn Allen, Rico Meinl, J. Sebastian Paez, Brian C. Searle, Seth Just, Lindsay K. Pino, William E. Fondrie
Summary: This study presents an open-source NextFlow pipeline, nf-encyclopedia, which connects three open-source tools (MSConvert, EncyclopeDIA, and MSstats) for analyzing DIA proteomics experiments with or without chromatogram libraries. The pipeline is reproducible and provides robust peptide and protein quantification. MSstats improves protein-level quantification performance over EncyclopeDIA alone.
JOURNAL OF PROTEOME RESEARCH
(2023)