Review
Chemistry, Analytical
A. Fernez Asensio, E. Alvarez-Gonzalez, A. Rodriguez, L. M. Sierra, E. Blanco-Gonzalez
Summary: Dysregulation of TCA cycle enzymes leads to abnormal accumulation of oncometabolites, which contribute to cancer formation and progression. GC-MS and LC-MS are powerful analytical tools for accurate identification and determination of these metabolites.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Analytical
Kevin Jooss, Luis F. Schachner, Rachel Watson, Zachary B. Gillespie, Sarah A. Howard, Marcus A. Cheek, Matthew J. Meiners, Amin Sobh, Jonathan D. Licht, Michael-Christopher Keogh, Neil L. Kelleher
Summary: The study introduces a new platform for separating and characterizing whole nucleosomes and their modifications, aiding in understanding epigenetic regulatory mechanisms. The platform offers low sample requirements and costs, with high detection sensitivity.
ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Analytical
Ketki Bagwe, Noah Gould, Kendall R. Johnson, Alexander R. Ivanov
Summary: Tissues and cell populations exhibit high levels of heterogeneity at the cellular level, making it important to analyze smaller sample sizes to capture subtle differences between cells. Capillary electrophoresis coupled with mass spectrometry (CE-MS) is a powerful technique for proteomics and metabolomics analysis at the single-cell level, and this review focuses on its applications and recent advances in sample preparation, separation, MS acquisition, and data analysis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Albert Perez-Alcaraz, Francesc Borrull, Marta Calull, Carme Aguilar
Summary: The consumption of synthetic cathinones has been increasing in recent years due to its affordability and accessibility as an alternative to amphetamines. Developing procedures capable of detecting and monitoring their consumption is crucial, and urine has been widely used for this purpose as it is non-invasive and provides larger sample volumes than other biological matrices. Chromatographic techniques are the most reported approach for determining cathinones in urine samples.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Kemilly M. P. Pinheiro, Alysson V. F. Sako, Marcella F. Rodrigues, Boniek G. Vaz, Iris Medeiros Junior, Rogerio M. Carvalho, Wendell K. T. Coltro
Summary: A capillary electrophoresis-mass spectrometry method was developed for the analysis of naphthenic acids in produced water samples. The method showed good repeatability and linear behavior within certain concentration ranges for different acids. It successfully identified and quantified the targeted acids in real water samples, demonstrating its effectiveness in complex sample analysis.
JOURNAL OF SEPARATION SCIENCE
(2023)
Review
Chemistry, Analytical
Justyna Piechocka, Rafal Glowacki
Summary: This overview summarizes all documented analytical methods for the quantification of homocysteine thiolactone (HTL) in biological samples, with a focus on pre-analytical treatment strategies and separation techniques. The review also discusses the advantages, pitfalls, and limitations of the methods, as well as the origin and main metabolites of HTL, and the association between civilization diseases and sulfur-containing compounds' metabolism disorders.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Qinlei Liu, Sandra Martinez-Jarquin, Wenjie Ge, Renato Zenobi
Summary: Understanding diseases requires understanding metabolic heterogeneity in cells. This technical note introduces a 3D printing technology for manufacturing an ionization source for mass spectrometry-based single-cell analysis. The all in-one 3D-printed electrospray ionization source simplifies the process and improves reproducibility. It has been successfully used for high-throughput analysis of cancer cells and can be adjusted for different cell sizes. This 3D-printed ionization source opens new possibilities for single-cell analysis.
ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Susanna Della Posta, Chiara Fanali, Valeria Gallo, Salvatore Fanali
Summary: This paper presents recent results obtained by coupling electromigration techniques with mass spectrometry, highlighting the advantages of this hybrid approach and discussing selected applications.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Radim Polasek, Klara Konderlova, Jan Petr
Summary: The aim of this study was to develop a new method for analyzing tamsulosin enantiomers using capillary electrophoresis combined with tandem mass spectrometry. The method achieved a limit of detection of 1.6 nmol L-1 under optimal conditions. It was validated for linearity, detection and quantification limits, precision, recovery, and selectivity, and can be applied to the analysis of tamsulosin enantiomers in environmental samples and other analytical tasks.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Analytical
Bo Liu, Wentao Wang, Tie Gao, Lu Huang, Huihong Fan, Hong-Xu Chen
Summary: Cobratide, a peptide drug extracted from Chinese cobra venom, has shown potential in treating not only chronic pain but also COVID-19. A protocol combining sheathless CE-MS and CE-UV methods was established for the separation, identification, and quantification of cobratide and its impurities, providing valuable information for quality control and process analysis of peptide drugs.
ANALYTICAL METHODS
(2021)
Article
Biochemical Research Methods
Katarzyna Pauter, Malgorzata Szultka-Mlynska, Michal Szumski, Anna Krol-Gorniak, Pawel Pomastowski, Boguslaw Buszewski
Summary: A new analytical method was developed and validated for simultaneous analysis of antibiotic drugs and their metabolites in human urine using capillary electrophoresis and tandem mass spectrometry. The method was linear and accurate for concentrations ranging from 20 to 1000 ng/mL.
Review
Chemistry, Analytical
Stanislava Rakusanova, Tomas Cajka
Summary: This article reviews the current analytical methods for analyzing type 2 diabetes (T2D) medication in human and animal samples. The advantages and limitations of sample preparation, separation, and detection of these drugs are discussed. The importance of multi-targeted analytical methods and assessing T2D medication adherence is emphasized.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Hanne Roberg-Larsen, Steven Ray Wilson, Elsa Lundanes
Summary: This review focuses on the application of nLC-MS in sample preparation, particularly through online upfront devices and online reaction systems to improve the sensitivity and robustness of samples.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Albert Perez-Alcaraz, Francesc Borrull, Carme Aguilar, Marta Calull, Fernando Benavente
Summary: This study introduces an in-line solid-phase extraction capillary electrophoresis-mass spectrometry (SPE-CE-MS) method for enantiodetermination of drugs of abuse in urine samples, specifically achieving enantioseparation of R,S-3,4-methylenedioxypyrovalerone (R,S-MDPV). The developed method is sensitive and accurate for analyzing urine samples.
Review
Chemistry, Multidisciplinary
Siyu Chen, Weibo Huang, Yunliang Qiu, Xueji Zhang, Jinming Kong
Summary: This paper describes the mechanism of action and drug metabolism process of flunitrazepam, reviews the different methods for detecting flunitrazepam published over the years, summarizes the detection limits of each method and compares their advantages and disadvantages. We hope to provide some inspiration for future research in this field.
Article
Immunology
Farhan Basit, Tom van Oorschot, Jessie van Buggenum, Rico J. E. Derks, Sarantos Kostidis, Martin Giera, I. Jolanda M. de Vries
Summary: Dendritic cells play a crucial role in connecting innate and adaptive immunity by presenting antigens to T cells and activating cytotoxic T-cell responses. This study found that TLR stimulation altered the metabolism and lipid composition of conventional DC type 1, reducing glycolysis gene expression and increasing oxidative phosphorylation.
Article
Food Science & Technology
Madhushri S. Varunjikar, Carlos Moreno-Ibarguen, Juan S. Andrade-Martinez, Hui-Shan Tung, Ikram Belghit, Magnus Palmblad, Pal A. Olsvik, Alejandro Reyes, Josef D. Rasinger, Kai K. Lie
Summary: The study shows that both DNA and protein-based approaches can efficiently tackle current challenges in feed and food authentication analyses.
Article
Biochemical Research Methods
Aries Aisporna, H. Paul Benton, Andy Chen, Rico J. E. Derks, Jean Marie Galano, Martin Giera, Gary Siuzdak
Summary: Neutral loss (NL) spectral data is a valuable resource for molecular discovery and similarity analysis. Researchers have created a MS2 to NL converter and developed the METLIN-NL database to enhance unknown identification and complement existing fragment ion databases.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Microbiology
Shraddha Shitut, Meng-Jie Shen, Bart Claushuis, Rico J. E. Derks, Martin Giera, Daniel Rozen, Dennis Claessen, Alexander Kros
Summary: Cell fusion is an important biological process that leads to the mixing of cellular contents and the formation of multinuclear cells. It holds promise for biotechnological innovations, such as the discovery of new antibiotics. This study investigated cell-cell fusion using antibiotic-producing bacteria as a model and found that fusion between genetically distinct cells can result in viable heterokaryons with increased antimicrobial activity. The rate of fusion was dependent on membrane fluidity, which is related to lipid composition as a function of cellular age. Furthermore, targeted fusion between distinctly marked cells was achieved using synthetic membrane-associated lipopeptides, providing a potential strategy for enhancing fusion efficiency and discovering new drugs.
MICROBIOLOGY SPECTRUM
(2022)
Editorial Material
Biochemical Research Methods
Benjamin A. Neely, Magnus Palmblad
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Rob Marissen, Madhushri S. Varunjikar, Jeroen F. J. Laros, Josef D. Rasinger, Benjamin A. Neely, Magnus Palmblad
Summary: In this paper, the authors present an update to a method and software tool for species identification based on mass spectrometry data. The method has been widely used in various applications and now includes a new metric and graphical user interface.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Tobias G. Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaino, Eric W. Deutsch
Summary: Data set acquisition and curation are challenging in machine learning, particularly for proteomics-based LC-MS data sets due to data reduction. ProteomicsML is introduced as an online resource for accessing proteomics-based data sets and tutorials. It simplifies data access and provides tutorials for interacting with advanced algorithms. ProteomicsML enables comparison of machine learning algorithms and offers introductory material for newcomers in the field. The platform is freely available at https://www.proteomicsml.org/, and contributions are welcome at https://github.com/ProteomicsML/ProteomicsML.
JOURNAL OF PROTEOME RESEARCH
(2023)
Editorial Material
Biochemical Research Methods
Michael R. Hoopmann, Veit Schwaemmle, Magnus Palmblad
JOURNAL OF PROTEOME RESEARCH
(2023)
Editorial Material
Biochemical Research Methods
John R. Yates, Ileana M. Cristea, Meng-Qui Dong, Claire E. Eyers, Joshua LaBaer, Jia V. Li, Jeremy K. Nicholson, Christopher M. Overall, Magnus Palmblad, Nikolai Slavov
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Sara Forcisi, Franco Moritz, Christopher J. Thompson, Basem Kanawati, Jenny Uhl, Carlos Afonso, Chantal D. Bader, Aiko Barsch, Berin A. Boughton, Rosalie K. Chu, Justine Ferey, Francisco Fernandez-Lima, Celine Gueguen, Dimitri Heintz, Mario Gomez-Hernandez, Kyoung-Soon Jang, Nikolas Kessler, Vaughn Mangal, Rolf Mueller, Ryo Nakabayashi, Edith Nicol, Simone Nicolardi, Magnus Palmblad, Ljiljana Pasa-Tolic, Jacob Porter, Isabelle Schmitz-Afonso, Jong Bok Seo, Eduardo Sommella, Yuri E. M. van der Burgt, Claire Villette, Matthias Witt, Ashley Wittrig, Jeremy J. Wolff, Michael L. Easterling, Frank H. Laukien, Philippe Schmitt-Kopplin
Summary: Ultrahigh resolution mass spectrometry combined with direct infusion ionization is a fast and accurate method for untargeted metabolomics analysis. Fourier transform ion cyclotron resonance mass spectrometers play an important role in studying complex chemical systems by enabling unambiguous molecular formula assignment. Through a comparison study involving 17 laboratories worldwide, we found that five laboratories showed comparable and representative performances, providing a reference for future ring trials on blood plasma.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
K. Madunic, Y. M. C. A. Luijkx, O. A. Mayboroda, G. M. C. Janssen, P. A. van Veelen, K. Strijbis, T. Wennekes, G. S. M. Lageveen-Kammeijer, M. Wuhrer
Summary: This study identified specific mucin O-glycans that mark butyrate-induced epithelial differentiation of the intestinal cell line CaCo-2 using porous graphitized carbon nano-liquid chromatography with electrospray ionization tandem mass spectrometry. The results showed that the fully differentiated butyrate-stimulated cells have a higher expression of sialylated O-glycan structures, while fucosylation is downregulated during differentiation. These findings provide insights into the dynamic O-glycosylation patterns in the gut and their functional role in gut-microbiota homeostasis and dysbiosis.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Review
Chemistry, Analytical
Magnus Palmblad, Reinier Vleugels, Jonas Bergquist
Summary: Capillary electrophoresis has become a highly sensitive and widely used analytical method. In this study, text mining and computational chemistry were used to analyze the scientific literature on capillary electrophoresis, revealing both expected and unexpected details. All software and data used in this study are freely available on GitHub and OSF.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Magnus Palmblad, Nees Jan van Eck, Jonas Bergquist
Summary: Using bibliometric methods, we have explored the history of capillary electrophoresis. The analysis reveals a co-authorship network of 416 prolific researchers connected by publications between 1980 and 2021. Research topics include electrochemistry, sensors, nanotechnology, and metabolomics, indicating the maturity of capillary electrophoresis technology. Citation patterns show strong coupling between journals of similar scope. Interactive versions of the bibliometric network visualizations are available online.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Oleg A. Mayboroda, Guinevere S. M. Lageveen-Kammeijer, Manfred Wuhrer, Radboud J. E. M. Dolhain
Summary: Rheumatoid arthritis (RA) is a prevalent autoimmune disease affecting joints and other organs. Glycosylation changes in immunoglobulin G (IgG) and immunoglobulin A (IgA) have been found in RA patients, which can be used as biomarkers to differentiate patients and predict disease activity.