Article
Biochemical Research Methods
Guangyong Yang, Jingxi Guo, Hui Yuan, Lei Sun, Lina Sha
Summary: In this study, a method based on ultra-performance convergence chromatography-triple quadrupole mass spectrometry (UPC2-MS/MS) was developed to detect 63 glucocorticoids in healthy foods. The method showed good linearity, low detection limits, and better selectivity and resolution compared to the traditional reverse-phase liquid chromatography-mass spectrometry (RPLC-MS/MS) method. The study provides new technical support for assessing the risk of exposure to glucocorticoids in healthy foods.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Analytical
Xinwen Zhang, Xiang Lv, Dong Qian, Junxian Li, Yi Qian, Jiaojiao Wang, Yuyu Zhu, Jing Zhou, Hongyue Ma
Summary: This research developed a quantitative approach using peptides to assess the quality of cinobufacini preparations. 230 peptides in cinobufacini injection were identified and a quantitative method for species-specific peptides was established. The quality of cinobufacini injection was found to be generally stable and the toad skin from Shandong was of the best quality.
JOURNAL OF SEPARATION SCIENCE
(2023)
Article
Food Science & Technology
Ainhoa Oller-Ruiz, Natalia Campillo, Manuel Hernandez-Cordoba, Javier Gilabert, Pilar Vinas
Summary: The study proposed using DLLME for preconcentration of lipophilic marine toxins in seawater samples. By optimizing the parameters and validating the method through recovery studies, the analysis showed that the water samples were free of the studied toxins.
Article
Chemistry, Analytical
Adam P. Huntley, Adam L. Hollerbach, Aneesh Prabhakaran, Sandilya V. B. Garimella, Cameron M. Giberson, Randolph Norheim, Richard D. Smith, Yehia M. Ibrahim
Summary: This work demonstrates a method to enhance the sensitivity of ion mobility (IM)-selected ions by accumulating them in a series of high-capacity ion traps inside a novel SLIMIMS module. Each ion trap can be used to extract peak ions from an ion mobility separation. Ions can be stored without losses for long times and released all at once or one by one.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Maarten Degreef, Eleanor M. Berry, Adrian Covaci, Kristof E. K. Maudens, Alexander L. N. van Nuijs
Summary: This study compares two easy-to-use screening methods for routine toxicological analysis. After analyzing 105 medico-legal case samples, it was found that both methods are effective for screening most compounds in toxicological analysis. The semi-quantitative analysis using the tMRM method with a small number of labeled internal standards yielded excellent results, while the semi-quantitative analysis using the QTOF method was more time-consuming.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2022)
Article
Chemistry, Analytical
Alaa Riezk, Vasin Vasikasin, Richard C. C. Wilson, Timothy M. M. Rawson, James G. G. McLeod, Rishi Dhillon, Jamie Duckers, Anthony E. G. Cass, Alison H. H. Holmes
Summary: This study aimed to establish and validate a rapid and reliable liquid chromatography-tandem mass spectrometry (LC/MS) method for the simultaneous quantification of cefiderocol and meropenem in human plasma of critically ill patients. The method involved protein precipitation using acetonitrile for sample clean-up, followed by reverse phase chromatography using triple quadrupole LC/MS. The developed method showed good linearity, accuracy, and sensitivity for both cefiderocol and meropenem, with stability at different temperatures and protein binding assessed in human plasma.
ANALYTICAL METHODS
(2023)
Article
Multidisciplinary Sciences
Estrella Sanz Rodriguez, Shing Lam, Gregory G. Smith, Paul R. Haddad, Brett Paull
Summary: This study described a method for the direct, robust, accurate, and highly sensitive detection of oxyhalide species in natural waters, including seawater, using suppressed ion chromatography coupled with mass spectrometry. The method demonstrated practical utility in monitoring changes to seawater composition following disinfection treatments, with iodate, bromate, and chlorate detected as the main oxyanionic disinfection by-products.
Article
Chemistry, Analytical
Rui Guo, Qisheng Zhong, Jiaqi Liu, Peiming Bai, Zongpeng Wang, Jieling Kou, Peijie Chen, Jie Zhang, Bo Zhang
Summary: In this study, a method called 2D-LC/TQMS was developed for simultaneous analysis of hydrophilic and hydrophobic metabolites using the combination of HILIC and RPLC. The method can detect 417 metabolites involved in various metabolic pathways with good reproducibility, linearity, and wide linear range. It was tested using different biological samples and applied to a bladder cancer case/control study, identifying 30 differential metabolites related to carbohydrate and amino acid metabolism.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Chaohui Qiu, Xiaolong Li, Zhe Li, Liu Yang, Weimin Wang, Chuan-Fan Ding, Fuxing Xu
Summary: This paper explores three new profile quadrupole ion funnels (QIF) to improve the transmission efficiency of low m/z ions.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Patric Lindahl, Grzegorz Olszewski, Mats Eriksson
Summary: The study evaluated and optimized the stability of uranium isotopic ratios measurements using the Agilent 8900 triple quadrupole inductively coupled plasma mass spectrometry (ICP-MS/MS) system. By adjusting the mass filter resolution settings, considerable improvement in precision and accuracy was achieved, with precision of 0.07% for long-term measurement of U-233/U-235 ratios.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2021)
Article
Environmental Sciences
Yaotian Wang, Haiyan Zhang, Xingwang Hou, Qing Zhang, Weifang Chen, Jianbo Shi, Guibin Jiang
Summary: A sensitive method for simultaneous determination of nine polyCBD congeners in shellfish was developed and applied to samples from markets in eight coastal cities in China. The results showed low contamination of HCBD in the marketed shellfish and fish, laying the groundwork for future research on the environmental behavior and exposure risks of polyCBDs in aquatic biotas.
ENVIRONMENTAL POLLUTION
(2021)
Article
Chemistry, Analytical
Wenting Bu, Liang Yang, Lei Tang, Ke Xiong, Youyi Ni, Chuting Yang, Sheng Hu
Summary: Monitoring ultra-trace levels of Tc-99 in environmental samples is crucial for assessing radioactivity and tracing oceanographic processes. We introduced a new method for measuring Tc isotopes using triple quadrupole ICP-MS/MS. By introducing O-2 gas, we were able to eliminate isobaric interference from Mo-97 and achieve high separation between Mo and Tc.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Estrella Sanz Rodriguez, Kyra Wood, Paul R. Haddad, Brett Paull
Summary: This study presents a simple, rapid, and reliable method for determining boron in aqueous solutions using suppressed ion chromatography coupled to electrospray ionisation-triple quadrupole mass spectrometry. The method achieved a low limit of detection and demonstrated excellent analytical performance.
Article
Chemistry, Analytical
Nathaniel D. Fletcher, Benjamin T. Manard, Debra A. Bostick, William D. Bostick, Shalina C. Metzger, Brian W. Ticknor, Kayron T. Rogers, Cole R. Hexel
Summary: The analysis of impurities in a uranium ore concentrate (UOC) provides valuable information on the source, production history, and potential intended use. Concentrations of phosphorus and sulfur were determined by mass spectrometry and compared to results from a pyrohydrolysis method. The method allows for the removal of interferences in the analysis of species in UOC materials.
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
Oncology
Liang-Bo Wang, Alla Karpova, Marina A. Gritsenko, Jennifer E. Kyle, Song Cao, Yize Li, Dmitry Rykunov, Antonio Colaprico, Joseph H. Rothstein, Runyu Hong, Vasileios Stathias, MacIntosh Cornwell, Francesca Petralia, Yige Wu, Boris Reva, Karsten Krug, Pietro Pugliese, Emily Kawaler, Lindsey K. Olsen, Wen-Wei Liang, Xiaoyu Song, Yongchao Dou, Michael C. Wendl, Wagma Caravan, Wenke Liu, Daniel Cui Zhou, Jiayi Ji, Chia-Feng Tsai, Vladislav A. Petyuk, Jamie Moon, Weiping Ma, Rosalie K. Chu, Karl K. Weitz, Ronald J. Moore, Matthew E. Monroe, Rui Zhao, Xiaolu Yang, Seungyeul Yoo, Azra Krek, Alexis Demopoulos, Houxiang Zhu, Matthew A. Wyczalkowski, Joshua F. McMichael, Brittany L. Henderson, Caleb M. Lindgren, Hannah Boekweg, Shuangjia Lu, Jessika Baral, Lijun Yao, Kelly G. Stratton, Lisa M. Bramer, Erika Zink, Sneha P. Couvillion, Kent J. Bloodsworth, Shankha Satpathy, Weiva Sieh, Simina M. Boca, Stephan Schurer, Feng Chen, Maciej Wiznerowicz, Karen A. Ketchum, Emily S. Boja, Christopher R. Kinsinger, Ana Robles, Tara Hiltke, Mathangi Thiagarajan, Alexey Nesvizhskii, Bing Zhang, D. R. Mani, Michele Ceccarelli, Xi S. Chen, Sandra L. Cottingham, Qing Kay Li, Albert H. Kim, David Fenyo, Kelly Ruggles, Henry Rodriguez, Mehdi Mesri, Samuel H. Payne, Adam C. Resnick, Pei Wang, Richard D. Smith, Antonio Iavarone, Milan G. Chheda, Jill S. Barnholtz-Sloan, Karin D. Rodland, Tao Liu, Li Ding
Summary: Understanding the molecular pathogenesis of glioblastoma is crucial for improving diagnosis and treatment. Integrated analysis of genomic, proteomic, and metabolomic data on treatment-naive glioblastomas has identified key phosphorylation events and potential targets for specific tumor alterations. Immune subtypes with distinct immune cell types were discovered, and specific histone acetylation patterns were correlated with these subtypes, providing insights for stratification of patients for more effective treatment.
Article
Biology
Chia-Feng Tsai, Pengfei Zhang, David Scholten, Kendall Martin, Yi-Ting Wang, Rui Zhao, William B. Chrisler, Dhwani B. Patel, Maowei Dou, Yuzhi Jia, Carolina Reduzzi, Xia Liu, Ronald J. Moore, Kristin E. Burnum-Johnson, Miao-Hsia Lin, Chuan-Chih Hsu, Jon M. Jacobs, Jacob Kagan, Sudhir Srivastava, Karin D. Rodland, H. Steven Wiley, Wei-Jun Qian, Richard D. Smith, Ying Zhu, Massimo Cristofanilli, Tao Liu, Huiping Liu, Tujin Shi
Summary: The SOP-MS method combines surfactants and mass spectrometry to achieve label-free global quantification of single-cell proteomics, effectively reducing surface adsorption losses and allowing for convenient measurement of hundreds of proteins from single cells, providing new opportunities for single-cell proteomics research.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemical Research Methods
James M. Fulcher, Aman Makaju, Ronald J. Moore, Mowei Zhou, David A. Bennett, Philip L. De Jager, Wei-Jun Qian, Ljiljana Pasa-Tolic, Vladislav A. Petyuk
Summary: The study focused on how to improve the depth of top-down proteomics (TDP) using high-field asymmetric waveform ion mobility spectrometry (FAIMS), enhancing protein coverage in Alzheimer's disease brain tissue samples and identifying amyloid beta proteoforms associated with Alzheimer's disease.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Plant Sciences
Kim K. Hixson, Joaquim V. Marques, Jason P. Wendler, Jason E. McDermott, Karl K. Weitz, Therese R. Clauss, Matthew E. Monroe, Ronald J. Moore, Joseph Brown, Mary S. Lipton, Callum J. Bell, Ljiljana Pasa-Tolic, Laurence B. Davin, Norman G. Lewis
Summary: The study on Arabidopsis ADT knock-out mutants revealed significant changes in lignin levels, affecting a range of metabolic pathways including protein synthesis. These findings support the idea of additional post-transcriptional and translational processes in lignin biosynthesis regulation, with new protein targets identified for further biochemical analysis and plant bioengineering. Additionally, functional categorizations of proteomics and transcriptomics analyses showed alterations in various metabolic pathways in the ADT KO mutants, highlighting potential targets for future research in plant biology.
FRONTIERS IN PLANT SCIENCE
(2021)
Correction
Multidisciplinary Sciences
Jongmin Woo, Sarah M. Williams, Lye Meng Markillie, Song Feng, Chia-Feng Tsai, Victor Aguilera-Vazquez, Ryan L. Sontag, Ronald J. Moore, Dehong Hu, Hardeep S. Mehta, Joshua Cantlon-Bruce, Tao Liu, Joshua N. Adkins, Richard D. Smith, Geremy C. Clair, Ljiljana Pasa-Tolic, Ying Zhu
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jongmin Woo, Sarah M. Williams, Lye Meng Markillie, Song Feng, Chai-Feng Tsai, Victor Aguilera-Vazquez, Ryan L. Sontag, Ronald J. Moore, Dehong Hu, Hardeep S. Mehta, Joshua Cantlon-Bruce, Tao Liu, Joshua N. Adkins, Richard D. Smith, Geremy C. Clair, Ljiljana Pasa-Tolic, Ying Zhu
Summary: This study introduces a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based single-cell proteomics workflow. The N2 chip enables robust quantification of approximately 1500 proteins and reveals membrane protein markers, demonstrating high stability of single-cell proteome profiles for cells cultured under identical conditions.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Xiaolu Li, Nicholas J. Day, Song Feng, Matthew J. Gaffrey, Tai-Du Lin, Vanessa L. Paurus, Matthew E. Monroe, Ronald J. Moore, Bin Yang, Ming Xian, Wei-Jun Qian
Summary: Thiol-based post-translational modifications play a crucial role in redox-dependent regulation and signaling, with functional cysteine sites serving as redox switches regulated through various types of PTMs. A direct detection workflow using LC-MS/MS was established to characterize the complexity of thiol PTMs at the proteome level, showing simultaneous quantification of protein abundances and different thiol PTMs. The study demonstrated the utility of this workflow by identifying over 9000 proteins and multiple types of thiol PTMs in mouse pancreatic beta-cells under ER stress, indicating independent translational and post-translational regulation of enzyme activity.
Article
Biochemistry & Molecular Biology
Jongmin Woo, Geremy C. Clair, Sarah M. Williams, Song Feng, Chia-Feng Tsai, Ronald J. Moore, William B. Chrisler, Richard D. Smith, Ryan T. Kelly, Ljiljana Pasa-Tolic, Charles Ansong, Ying Zhu
Summary: Single-cell proteomics (scProteomics) is a powerful tool for studying cell functions in complex biological systems. However, current methods face challenges in identifying and quantifying low-abundance proteins accurately. In this study, we present a method called transferring identification based on FAIMS filtering (TIFF), which combines ion mobility-enhanced mass spectrometry acquisition and peptide identification to improve the sensitivity and accuracy of label-free scProteomics. By filtering out singly charged ions, the TIFF method extends the ion accumulation times for peptide ions. Peptide identities are determined using a three-dimensional MS1 feature matching approach. Using TIFF, we achieved unbiased proteome analysis of over 1,700 proteins in single HeLa cells, with more than 1,100 proteins consistently identified. We also applied the TIFF method to study time-dependent proteome changes in single murine macrophage cells during lipopolysaccharide stimulation.
Article
Biochemistry & Molecular Biology
Nicholas J. Day, Tong Zhang, Matthew J. Gaffrey, Rui Zhao, Thomas L. Fillmore, Ronald J. Moore, George G. Rodney, Wei-Jun Qian
Summary: This study reports a deep redox proteome profiling workflow and demonstrates its application in measuring the changes in thiol oxidation and global protein expression in skeletal muscle from mdx mice. The results show that mdx mice exhibit significantly increased thiol oxidation, particularly in the coagulation system and immune-related pathways, while protein abundance changes are more enriched in pathways associated with bioenergetics.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Biochemical Research Methods
Adam C. Swensen, Dusan Velickovic, Sarah M. Williams, Ronald J. Moore, Le Z. Day, Sherry Niessen, Sarah Hennessy, Camilo Posso, Mara Monetti, Wei-Jun Qian, Jon Jacobs, Laurence Whiteley, Ying Zhu, Paul D. Piehowski
Summary: Despite their small size, islets of Langerhans play a crucial role in maintaining systemic energy balance in the body. This study uses advanced technologies to investigate the protein profiles of different features within the islet, revealing unique protein signatures in the inner vasculature that indicate increased innervation and intra-islet neuron-like crosstalk. The data also prove useful in identifying localized structure-specific drug-target interactions.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Chemistry, Analytical
Junho Park, Fengchao Yu, James M. Fulcher, Sarah M. Williams, Kristin Engbrecht, Ronald J. Moore, Geremy C. Clair, Vladislav Petyuk, Alexey I. Nesvizhskii, Ying Zhu
Summary: To overcome the issue of ratio compression in isobaric labeling-based multiplexed single-cell proteomics, we developed an improved MS3-based method using a linear ion trap. This method increased proteome coverage for single-cell-level peptides and was applied to study immune activation in single macrophages.
ANALYTICAL CHEMISTRY
(2023)
Meeting Abstract
Biochemical Research Methods
Chia-Feng Tsai, Yi-Ting Wang, Chuan-Chih Hsu, Reta B. Kitata, Rosalie K. Chu, Marija Velickovic, Rui Zhao, Sarai M. Williams, William B. Chrisler, Marda L. Jorgensen, Ronald J. Moore, Ying Zhu, Karin D. Rodland, Richard D. Smith, Clive H. Wasserfall, Tujin Shi, Tao Liu
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Yumi Kwon, Paul D. Piehowski, Rui Zhao, Ryan L. Sontag, Ronald J. Moore, Kristin E. Burnum-Johnson, Richard D. Smith, Wei-Jun Qian, Ryan T. Kelly, Ying Zhu
Summary: Spatial proteomics holds great promise for revealing tissue heterogeneity, but current workflows require large sample amounts that may blur cell-type or microstructure-specific information. In this study, an improved sample preparation method was developed to enhance sample recovery and enable more precise protein analysis by integration with established techniques.
Meeting Abstract
Oncology
Liang-Bo Wang, Alla Karpova, Marina A. Gritsenko, Jennifer E. Kyle, Song Cao, Yize Li, Dmitry Rykunov, Antonio Colaprico, Joseph Rothstein, Runyu Hong, Vasileios Stathias, MacIntosh Cornwell, Francesca Petralia, Richard D. Smith, Antonio Iavarone, Milan G. Chheda, Jill S. Barnholtz-Sloan, Karin D. Rodland, Tao Liu, Li Ding
Article
Biochemical Research Methods
Christopher R. Conant, Isaac K. Attah, Sandilya V. B. Garimella, Gabe Nagy, Aivett Bilbao, Richard D. Smith, Yehia M. Ibrahim
Summary: In this study, five different waveforms were characterized in terms of their transmission efficiency, IMS resolution, and resolving power, with triangle and asymmetric ramp profiles found to offer modestly greater resolution and resolving power compared to others. The research also revealed that separations were generally improved with higher TW amplitudes, moderately improved by lower speeds, but experienced decreases in signal intensity under extreme operating conditions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)