Article
Multidisciplinary Sciences
Kristine Korzow Richter, Maria C. Codlin, Melina Seabrook, Christina Warinner
Summary: Collagen peptide mass fingerprinting by MALDI-TOF-MS, also known as ZooMS, is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. It enables rapid taxonomic identification of large bone assemblages and cultural heritage objects. However, there are limitations that need to be addressed for future advancements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Samantha Brown, Katerina Douka, Matthew J. Collins, Kristine Korzow Richter
Summary: ZooMS, a peptide mass fingerprinting technique, is increasingly utilized in archaeological and cultural heritage science, but faces challenges due to inconsistent nomenclature for peptide markers. Standardized guidelines proposed here aim to provide a reliable and consistent naming system, supporting the growth of ZooMS across diverse vertebrate taxa.
JOURNAL OF PROTEOMICS
(2021)
Article
Biotechnology & Applied Microbiology
M. Moussa, E. Cauvin, A. Le Piouffle, O. Lucas, A. Bidault, C. Paillard, F. Benoit, B. Thuillier, M. Treilles, M. A. Travers, Celine Garcia
Summary: This study developed a MALDI-TOF MS method for rapid identification of a variety of Vibrio species in mollusk aquaculture, creating the EnviBase library with 120 main spectra projections. The EnviBase library was validated through a blind test on 100 Vibrio strains, successfully identifying the majority of the strains.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Food Science & Technology
Katrien Dierickx, Samantha Presslee, Virginia L. Harvey
Summary: This research presents an alternative proteomic technique for reliable species identification of fish specimens. The study demonstrates the efficacy of collagen peptide mass fingerprinting in identifying different tissue types of fish samples, highlighting its importance in detecting mislabelling fraud in the food chain.
Article
Microbiology
Teruyo Ojima-Kato, Satomi Nagai, Akane Fujita, Junko Sakata, Hiroto Tamura
Summary: Identification of microorganisms by MALDI-TOF MS has become popular in the past 20 years. The Strain Solution ver. 2 software with MALDI-TOF MS allows accurate discrimination of serotypes and strains beyond the genus and species level by creating a theoretical mass-based database. This study constructed a theoretical mass database with validated biomarkers for proteotyping Campylobacter jejuni and achieved promising results.
Article
Microbiology
Claudia Honsig, Brigitte Selitsch, Marlene Hollenstein, Matthias G. Vossen, Kathrin Spettel, Birgit Willinger
Summary: In this study, the identification of 230 filamentous fungi isolates using MALDI-TOF MS in combination with the Filamentous Fungi Library 3.0 was investigated. The results showed that using the more time-consuming sample preparation methods improved species-level identification rates, and the in-house threshold for species identification was validated for routine use in the laboratory. This suggests that this commercial platform is suitable for routine diagnosis.
Review
Chemistry, Analytical
Hugo M. Santos, Luis B. Carvalho, Carlos Lodeiro, Goncalo Martins, Ines L. Gomes, Wilson D. T. Antunes, Vanessa Correia, Maria M. Almeida-Santos, Helena Rebelo-de-Andrade, Antonio P. A. Matos, J. L. Capelo
Summary: This work presents a tutorial on the capabilities of bioanalytical mass spectrometry in detecting and differentiating viruses at the peptide level, as well as providing diagnosis and prognosis for infected patients. It offers insights into the possibilities of current high-resolution mass spectrometry technology and bioinformatics.
MICROCHEMICAL JOURNAL
(2023)
Article
Chemistry, Organic
Bernard Fernandez, Jean Armengaud, Gilles Subra, Christine Enjalbal
Summary: This study investigates the feasibility of using high energy charge remote fragmentations to analyze the N-terminus of proteins, and compares it with low energy collision-induced dissociations. The results show that the amino acid composition significantly affects the dissociation pathways of peptide backbones.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemical Research Methods
Yi-Shan Li, Jau-Ling Suen, Wei-Lung Tseng, Chi-Yu Lu
Summary: The study developed a peptide probe for the detection of acrylamide by MALDI-TOF MS, which allows for detection in small sample volumes with a limit of detection as low as 0.05 ng/mu L without the need for organic solvents. The developed method showed a relative standard deviation and relative error of < 6.7% for intra- and inter-day assays.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Microbiology
Gyu Ri Kim, Si Hyun Kim, Eun-Young Kim, Eun Hee Park, In Yeong Hwang, Seok Hoon Jeong, Hyun Soo Kim, Young Ah Kim, Young Uh, Kyeong Seob Shin, Young Ree Kim, Namhee Ryoo, Jong Hee Shin, Jeong Hwan Shin
Summary: This study evaluated the usefulness of MALDI-TOF VITEK MS for Salmonella identification. The results showed that VITEK MS could accurately identify most Salmonella species, but had lower accuracy in identifying typhoidal Salmonella and Salmonella enterica ssp. diarizonae isolates.
Article
Microbiology
Camila Morschbacher Wilhelm, Maiara dos Santos Carneiro, Everton Inamine, Afonso Luis Barth
Summary: This study aimed to evaluate an adaptation of the MBT-ASTRA technique for faster antimicrobial susceptibility testing. The adapted method showed high categorical agreement with the standard method, indicating its potential for rapid AST results.
MICROBIOLOGY SPECTRUM
(2023)
Review
Chemistry, Analytical
Judy Gopal, Manikandan Muthu
Summary: Mushrooms have transitioned from a luxury food to a widely accepted nutrient-rich food. Mushroom polysaccharides have become icons of mushroom bioactivity, and the analytical techniques for their analysis have been consolidated and summarized.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Applied
Tomoya Yoshinari, Aoi Sekine, Naoki Kobayashi, Yuzo Nishizaki, Naoki Sugimoto, Yukiko Hara-Kudo, Maiko Watanabe
Summary: This study used SDS-PAGE and MALDI-TOF MS to analyze the sources of 36 enzyme preparations (EPs), and found that 30 EPs had consistent sources with the manufacturer's information, 5 EPs showed high sequence similarity to closely-related species, and 6 enzymes could not be identified. This approach can rapidly determine the biological origin of enzymes and contribute to ensuring the safety of EPs.
FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT
(2023)
Article
Food Science & Technology
Eiseul Kim, Seung-Min Yang, Hyun-Jae Kim, Hae-Yeong Kim
Summary: In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with in-house databases was used to distinguish between Enterococcus faecium and Enterococcus lactis. Specific mass peaks were identified for each species, providing a highly accurate and high-throughput alternative to 16S rRNA sequencing.
Article
Materials Science, Characterization & Testing
Tibor Nagy, Akos Kuki, Gergo Roth, Zuura Kaldybek Kyzy, Alifya Balqis Zatalini, David Nyul, Miklos Zsuga, Sandor Keki
Summary: In this study, Mass-remainder analysis (MARA) and Multi-step Mass-remainder analysis (M-MARA) were used to analyze polyacrylamide block copolymers. The choice of MARA base mass unit affects the plot shape and enables conclusions about block length and diversity. 2-step M-MARA plots provide even better visualization.
Article
Hematology
Yingchi Zhang, Yufeng Gao, Hui Zhang, Jingliao Zhang, Fuhong He, Ales Hnizda, Maoxiang Qian, Xiaoming Liu, Yoshihiro Gocho, Ching-Hon Pui, Tao Cheng, Qianfei Wang, Jun J. Yang, Xiaofan Zhu, Xin Liu
Article
Oncology
Ales Hnizda, Milan Fabry, Takaya Moriyama, Petr Pachl, Michael Kugler, Vitezslav Brinsa, David B. Ascher, William L. Carroll, Petr Novak, Marketa Zaliova, Jan Trka, Pavlina Rezacova, Jun J. Yang, Vaclav Veverka
Article
Rheumatology
Marie Zikanova, Dawn Wahezi, Arielle Hay, Blanka Stiburkova, Charles Pitts, Dita Musalkova, Vaclava Skopova, Veronika Baresova, Olga Souckova, Katerina Hodanova, Martina Zivna, Viktor Stranecky, Hana Hartmannova, Ales Hnizda, Anthony J. Bleyer, Stanislav Kmoch
Article
Multidisciplinary Sciences
Meirong Bai, Roman Vozdek, Ales Hnizda, Chenxiao Jiang, Bingying Wang, Ladislav Kuchar, Tiejun Li, Yuefan Zhang, Chase Wood, Liang Feng, Yongjun Dang, Dengke K. Ma
NATURE COMMUNICATIONS
(2018)
Article
Urology & Nephrology
Benjamin Cochran, Tereza Kovacikova, Katerina Hodanova, Martina Zivna, Ales Hnizda, Angela G. Niehaus, Alex Bonnecaze, Gowrie Balasubraminiam, Irene Ceballos-Picot, Amret Hawfield, Kendrah Kiddy, Stanislav Kmoch, Anthony J. Bleyer
CLINICAL NEPHROLOGY
(2018)
Article
Biochemistry & Molecular Biology
Petr Man, Milan Fabry, Irena Sieglova, Daniel Kavan, Petr Novak, Ales Hnizda
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2019)
Article
Biochemistry & Molecular Biology
Ales Hnizda, Tom L. Blundell
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2019)
Article
Oncology
Takaya Moriyama, Shuguang Liu, Jing Li, Julia Meyer, Xujie Zhao, Wentao Yang, Youming Shao, Richard Heath, Alet Hnizda, William L. Carroll, Jun J. Yang
MOLECULAR CANCER THERAPEUTICS
(2019)
Article
Biochemistry & Molecular Biology
Anna Pelet, Vaclava Skopova, Ulrike Steuerwald, Veronika Baresov, Mohammed Zarhrate, Jean-Marc Plaza, Ales Hnizda, Matyas Krijt, Olga Souckova, Flemming Wibrand, Guorio Andorsdottir, Frooi Joensen, David Sedlak, Anthony Bleyer, Stanislav Kmoch, Stanislas Lyonnet, Marie Zikanov
HUMAN MOLECULAR GENETICS
(2019)
Article
Urology & Nephrology
Martina Zivna, Kendrah Kidd, Mohamad Zaidan, Petr Vyletal, Veronika Baresova, Katerina Hodanova, Jana Sovova, Hana Hartmannova, Miroslav Votruba, Helena Treslova, Ivana Jedlickova, Jakub Sikora, Helena Hulkova, Victoria Robins, Ales Hnizda, Jan Zivny, Gregory Papagregoriou, Laurent Mesnard, Bodo B. Beck, Andrea Wenzel, Kalman Tory, Karsten Haeeffner, Matthias T. F. Wolf, Michael E. Bleyer, John A. Sayer, Albert C. M. Ong, Lidia Balogh, Anna Jakubowska, Agnieszka Laszkiewicz, Rhian Clissold, Charles Shaw-Smith, Raj Munshi, Robert M. Haws, Claudia Izzi, Irene Capelli, Marisa Santostefano, Claudio Graziano, Francesco Scolari, Amy Sussman, Howard Trachtman, Stephane Decramer, Marie Matignon, Philippe Grimbert, Lawrence R. Shoemaker, Christoforos Stavrou, Mayssa Abdelwahed, Neila Belghith, Matthew Sinclair, Kathleen Claes, Tal Kopel, Sharon Moe, Constantinos Deltas, Bertrand Knebelmann, Luca Rampoldi, Stanislav Kmoch, Anthony J. Bleyer
KIDNEY INTERNATIONAL
(2020)
Article
Biochemistry & Molecular Biology
Amanda K. Chaplin, Steven W. Hardwick, Shikang Liang, Antonia Kefala Stavridi, Ales Hnizda, Lee R. Cooper, Taiana Maia De Oliveira, Dimitri Y. Chirgadze, Tom L. Blundell
Summary: The study reveals the mechanism of how DNA-PKcs and the Ku70/80 heterodimer interact with DNA to repair DNA double-strand breaks, providing new insights into NHEJ.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Roopa Thapar, Jing L. Wang, Michal Hammel, Ruiqiong Ye, Ke Liang, Chengcao Sun, Ales Hnizda, Shikang Liang, Su S. Maw, Linda Lee, Heather Villarreal, Isaac Forrester, Shujuan Fang, Miaw-Sheue Tsai, Tom L. Blundell, Anthony J. Davis, Chunru Lin, Susan P. Lees-Miller, Terence R. Strick, John A. Tainer
NUCLEIC ACIDS RESEARCH
(2020)
Review
Biochemistry & Molecular Biology
Shikang Liang, Amanda K. Chaplin, Antonia Kefala Stavridi, Robert Appleby, Ales Hnizda, Tom L. Blundell
Summary: This paragraph discusses the three structural aspects of the repair pathway for Non-homologous end joining (NHEJ), emphasizing the orchestration of DNA repair to ensure robust and efficient NHEJ. It also highlights the focus on structural studies over the past two decades, utilizing both X-ray diffraction and cryo-EM techniques to investigate macromolecular assemblies.
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ales Hnizda, Petr Tesina, Thanh-Binh Nguyen, Zdenek Kukacka, Lukas Kater, Amanda Chaplin, Roland Beckmann, David B. Ascher, Petr Novak, Tom L. Blundell
Summary: Nonhomologous end joining (NHEJ) is a DNA repair mechanism that maintains genomic integrity, with the Ku70/80 complex playing a critical role in recognizing DNA breaks. Research has shown that the SAP domain in the Ku70 C-terminal region changes its position depending on DNA binding, potentially serving as a flexible entry gate for broken DNA.
Meeting Abstract
Biochemistry & Molecular Biology
P. Melenovska, J. Sokolova, J. Krijt, R. Vozdek, A. Hnizda, J. Kraus, T. Majtan, V. Kozich
EUROPEAN JOURNAL OF HUMAN GENETICS
(2018)
Article
Physics, Atomic, Molecular & Chemical
Daniel D. Vallejo, Joseph L. Corstvet, Facundo M. Fernandez
Summary: Electrospray ionization (ESI) is a popular method for generating ions in mass spectrometry (MS). The use of triboelectric nanogenerators as power sources for ESI shows promise in improving the analytical capabilities. This review highlights the fundamentals of ESI driven by DC power supplies, the contrasting qualities to triboelectric nanogenerator power supplies, and its applications in forensics, metabolomics, and protein structure analysis.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2024)
Article
Physics, Atomic, Molecular & Chemical
Florian Kluibenschedl, Anna Ploner, Christina Meisenbichler, Robert Konrat, Thomas Mueller
Summary: Mass spectrometry imaging (MSI) is a powerful analytical technique for localizing chemicals on surfaces. A new interactive approach, called interactive mass spectrometry imaging (IMSI), has been developed using a pen-like ionization interface connected to a mass spectrometer. This approach allows for real-time tracking of the pen's motion on a surface to obtain chemical data. The IMSI method was successfully tested on inkjet-printed letters and mouse brain tissue samples.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2024)
Article
Physics, Atomic, Molecular & Chemical
Shubhangee S. Gaikwad, Saurabh D. Kalkate, Amruta A. Bankar, Amol S. Bansode
Summary: A stable high-performance thin layer chromatographic technique was developed and validated for estimating the content of Paracetamol and Prochlorperazine. The method was validated according to the International Conference on Harmonization requirements. The study also investigated the degradation products of the drugs.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2024)
Article
Physics, Atomic, Molecular & Chemical
Ioan Marginean
Summary: In this study, a coherent classification of electrospray axial regimes is provided based on non-linear fluid dynamics. This classification includes periodic, transient/chaotic, and stationary regimes, and emphasizes the importance of spray current measurements and electrospray characteristic curves in diagnosing the operation and transitions between these regimes. The effect of the electrospray operating regime on the mass spectrometer signal is also summarized.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2024)
Article
Physics, Atomic, Molecular & Chemical
Le Thao Anh Nguyen, Chris J. Bowen, Laura Burchill, Spencer J. Williams, Richard A. J. O'Hair
Summary: D-Cysteinolic acid (D-CA) is an important metabolite in the biosulfur cycle, while a structural isomer, (R)-3-amino-2-hydroxypropanesulfonate ((R)-AHPS), is less common. Through mass spectrometry and density-functional theory, this study reveals the fragmentation reactions of these two isomers and methods to distinguish them.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2024)
Article
Physics, Atomic, Molecular & Chemical
Frank J. Wensink, Deepak Pradeep, P. B. Armentrout, Joost M. Bakker
Summary: Methane and cyclopropane were reacted with Ru+ ions, and the resulting products were identified and characterized using mass spectrometry, IR action spectroscopy, and density functional theory calculations.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2024)
