Article
Chemistry, Analytical
Ci Wu, Jiao Lei, Fei Meng, Xingyao Wang, Cassandra J. Wong, Jiaxi Peng, Ge Lin, Anne-Claude Gingras, Junfeng Ma, Shen Zhang
Summary: This study explores the applicability of turboDDA for quantitative proteomics of trace samples and finds that turboDDA exhibits better sensitivity. The accuracy and reproducibility of iTRAQ-labeled trace samples are evaluated, showing improved quantification accuracy and reproducibility with turboDDA.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Mathias Kalxdorf, Torsten Mueller, Oliver Stegle, Jeroen Krijgsveld
Summary: IceR is a quantitative workflow for proteomics that combines high identification rates of data-dependent acquisition with low missing value rates, improving quantification precision, accuracy, reliability, and data completeness. Applied to plasma and single-cell proteomics data, IceR enhances the number of reliably quantified proteins, improves discriminability between single-cell populations, and allows reconstruction of a developmental trajectory.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Patrick Willems, Ursula Fels, An Staes, Kris Gevaert, Petra Van Damme
Summary: To study physiological responses in bacterial infections, an optimized hybrid library generation workflow for DIA mass spectrometry was found to significantly improve sensitivity and depth of protein detection, without the need for prior enrichment of bacterial pathogens.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Thy Truong, Kei G. I. Webber, S. Madisyn Johnston, Hannah Boekweg, Caleb M. Lindgren, Yiran Liang, Alissia Nydegger, Xiaofeng Xie, Tsz-Ming Tsang, D. A. Dasun N. Jayatunge, Joshua L. Andersen, Samuel H. Payne, Ryan T. Kelly
Summary: We developed a new method called wide window acquisition (WWA) that combines efficient sample preparation and ultra-low-flow liquid chromatography to quantify >3,000 proteins from single cells in rapid label-free analyses. WWA increased the number of identified proteins by about 40% compared to standard data-dependent acquisition. Utilizing this platform, we compared protein expression in HeLa cells with and without the essential autophagy gene atg9a, and found significant changes in 268 proteins related to innate immunity, vesicle trafficking, and protein degradation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Pharmacology & Pharmacy
Qian Zhang, Xue Li, Jun Li, Yuxia Hu, Jing Liu, Fang Wang, Wei Zhang, Fuhou Chang
Summary: The study found that QXWWD had strong inhibitory effects against Staphylococcus aureus, Enterococcus faecalis, and Streptococcus pneumoniae, as well as potential effectiveness in suppressing ear swelling and reducing inflammatory cytokine levels. QXWWD was found to be safe for topical use and could change skin microstructure, indicating potential therapeutic effects.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemical Research Methods
Zeyuan Zuo, Liu Cao, Louis-Felix Nothia, Hosein Mohimani
Summary: The study introduces an optimized data acquisition strategy, MS2Planner, which increases the annotation rate of metabolites by 38.6% compared to DDA. MS2Planner is 62.5% more sensitive and 9.4% more specific than DDA in collecting high-quality fragmentation spectra.
Article
Biology
Ghizal Siddiqui, Amanda De Paoli, Christopher A. MacRaild, Anna E. Sexton, Coralie Boulet, Anup D. Shah, Mitchell B. Batty, Ralf B. Schittenhelm, Teresa G. Carvalho, Darren J. Creek
Summary: A comprehensive spectral library for Plasmodium falciparum-infected RBCs has been created, measuring the abundance of peptides from both the parasite and RBC proteins. This library includes proteins from different RBC stages, the RBC compartment of trophozoite-iRBCs, and cytosolic fraction from uninfected RBCs. By using this library, semi-quantitative proteomics datasets have been generated to characterize different asexual parasite stages and compare drug-resistant and drug-sensitive parasites.
Article
Biochemical Research Methods
Magdalena Wilde, Julian Brehm, Michael Schwarzer, Jan B. Stoeckl, Christian Laforsch, Thomas Froehlich
Summary: Aquatic pollution is a growing problem that requires extensive research to understand its consequences and find solutions. The crustacean Daphnia is a key species in lake ecosystems, making it suitable for studying the effects of freshwater pollution. Proteome analysis of Daphnia is hindered by highly abundant proteins, but a new method based on LC-MS/MS analysis of whole daphnids and dissected Daphnia gut was established to improve proteome coverage. Using this method, researchers identified a large number of protein groups in Daphnia and Daphnia gut samples, demonstrating the effectiveness of the approach.
Article
Chemistry, Multidisciplinary
Yang Wang, Shuying Liu
Summary: This study introduces the BoxCar DDA method to increase the MS2 coverage in liquid chromatography-mass spectrometry. The results show that BoxCar DDA significantly improves the MS2 coverage and signal quality. This method helps improve the confidence of compound identification in untargeted metabolomics.
ARABIAN JOURNAL OF CHEMISTRY
(2023)
Article
Biochemical Research Methods
Weigang Ge, Xiao Liang, Fangfei Zhang, Yifan Hu, Luang Xu, Nan Xiang, Rui Sun, Wei Liu, Zhangzhi Xue, Xiao Yi, Yaoting Sun, Bo Wang, Jiang Zhu, Cong Lu, Xiaolu Zhan, Lirong Chen, Yan Wu, Zhiguo Zheng, Wangang Gong, Qijun Wu, Jiekai Yu, Zhaoming Ye, Xiaodong Teng, Shiang Huang, Shu Zheng, Tong Liu, Chunhui Yuan, Tiannan Guo
Summary: SubLib is a computational strategy for optimizing spectral library size specific to DIA data sets, leading to increased peptide precursor and protein group identifications. This strategy showed significant improvements in identification rates in both test datasets and a large number of carcinoma samples, demonstrating its effectiveness in enhancing proteome coverage in DIA-MS data.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Agriculture, Multidisciplinary
Meiyu Liu, Xiaoyan Xu, Xiaoyan Wang, Hongda Wang, Yueguang Mi, Xiumei Gao, Dean Guo, Wenzhi Yang
Summary: The study successfully constructed a PIL-based DDA strategy and applied it to the identification of ginsenosides. The results showed significant advantages of this strategy in identifying both known and unknown ginsenosides.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemical Research Methods
Alicia L. Richards, Kuei-Ho Chen, Damien B. Wilburn, Erica Stevenson, Benjamin J. Polacco, Brian C. Searle, Danielle L. Swaney
Summary: The study evaluates a DIA multiplexing approach that combines three proteolytic digests into a single sample, showing increased peptide and amino acid detections and practical utility for applications requiring critical sequence coverage such as protein isoform analysis.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Spectroscopy
Reta Birhanu Kitata, Jhih-Ci Yang, Yu-Ju Chen
Summary: Data-independent acquisition mass spectrometry (DIA-MS) is a highly reproducible proteome profiling method that generates permanent digital maps for retrospective analysis. Recent advancements have improved the sensitivity and coverage of DIA-MS. This review discusses the evolution of DIA-MS techniques, recent applications, and challenges.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Chemistry, Analytical
Asad Ali Siyal, Eric Sheng-Wen Chen, Hsin-Ju Chan, Reta Birhanu Kitata, Jhih-Ci Yang, Hsiung-Lin Tu, Yu-Ju Chen
Summary: The study presents a sample size-comparable library-based DIA approach, achieving higher protein group identification from small-size library compared to medium-size, large-size, and lung cancer resource spectral library. The approach shows good generality across different instruments and data analysis methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Franjo Martinkovic, Marin Popovic, Ozren Smolec, Vladimir Mrljak, Peter David Eckersall, Anita Horvatic
Summary: Comprehensive profiling of serum proteome using DIA-MS method was applied to analyze non-depleted serum samples of healthy and naturally Leishmania-infected dogs, resulting in the identification of 554 proteins, 140 of which showed significant differences in abundance. These proteins are involved in lipid metabolism, hematological abnormalities, immune response, and oxidative stress, providing valuable insights into the complex molecular basis of canine leishmaniosis. Our study demonstrates that DIA-MS is a preferred method for understanding pathophysiological processes in serum and biomarker development.
Review
Spectroscopy
Michael Caleb Bagley, Kenneth P. Garrard, David C. Muddiman
Summary: In the past 15 years, ambient ionization techniques, particularly matrix-assisted laser desorption electrospray ionization, have made significant advancements in mass spectrometry imaging. These techniques have been developed and improved with different laser systems and mass spectrometers, leading to transformative developments in the imaging platform.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Biochemical Research Methods
Ying Xi, Alexandria L. Sohn, Alena N. Joignant, Stephanie M. Cologna, Boone M. Prentice, David C. Muddiman
Summary: Mass spectrometry imaging (MSI) is an important analytical technique for reporting the spatial location and abundance of detected ions in various studies. However, the lack of consistency in data reporting creates challenges in comparing MSI data. To address this issue, a unified data reporting system called SMART is proposed, which aims to capture essential baseline information for MSI studies. The tutorial emphasizes the necessity of establishing a uniform reporting system to facilitate the interpretation and comparison of MSI data.
JOURNAL OF MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Hongxia Bai, Jeffrey G. Manni Sr, David C. Muddiman
Summary: Infrared laser used in mass spectrometry imaging often leads to nonuniform ablation due to its Gaussian profile, which decreases image quality. To address this issue, researchers integrated a diffractive optical element into the optical path to generate homogeneous intensity distribution, ensuring complete sample removal with laser pulses.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Seth M. Eisenberg, Kevan T. Knizner, David C. Muddiman
Summary: Mass spectrometry imaging (MSI) is an analytical technique that detects and visualizes thousands of m/z values in two- and three-dimensional space. Discriminating sample-related analytes from ambient ions conventionally requires manual investigation of each ion heatmap, which is time-consuming and subjective. In this study, an ion classification tool (ICT) was developed using object-based image analysis in MATLAB, which accurately classified ions as on-tissue or background based on binary conversion and the number of detected objects.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Correction
Biochemical Research Methods
David C. Muddiman
JOURNAL OF MASS SPECTROMETRY
(2023)
Correction
Biochemical Research Methods
David C. Muddiman
JOURNAL OF MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Alena N. N. Joignant, Ying Xi, David C. C. Muddiman
Summary: Biospecimens with flat surfaces are needed for laser-based mass spectrometry imaging. However, imperfections in the sampling stages and non-flat samples require a deeper understanding of the laser beam's depth of focus. This tutorial explores the parameters and equations that describe the depth of focus of a Gaussian laser beam and presents methods to address surface roughness exceeding the laser's depth of focus.
JOURNAL OF MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Russell R. Kibbe, David C. Muddiman
Summary: Profile data collection in mass spectrometry imaging (MSI) studies often results in large files and long processing times. This study compares profile and centroid data collection methods in high-resolution accurate mass MSI. The results show that centroid data collection improves mass measurement accuracy and lipid annotation sensitivity compared to profile data collection.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Mary F. Wang, Alexandria L. Sohn, Juhi Samal, Kevin Erning, Tatiana Segura, David C. Muddiman
Summary: Two preparatory methods for mass spectrometry imaging (MSI), fresh-frozen and sucrose-embedded, paraformaldehyde (PFA) fixed, were evaluated in terms of ion abundance, putative lipid identifications, and preservation of analyte spatial distributions. Sucrose-embedded, PFA-fixed tissues without an ice matrix showed significantly higher numbers of putatively identified lipid species in positive and negative ion modes compared to the traditional gold-standard fresh-frozen tissue preparation with an exogenous ice matrix. Sucrose-embedded tissues also demonstrated improved spatial distribution of ions. These findings support sucrose-embedding without ice matrix as an alternative preparatory technique for IR-MALDESI-MSI.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Tana V. Palomino, David C. Muddiman
Summary: This study presents a new rule that can predict the number of sialic acids on a glycan. By utilizing infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) in negative-ion mode mass spectrometry, the number of sialic acids on the glycan can be predicted based on the experimental isotopic distribution of a detected glycan. This new rule improves the capability of IR-MALDESI to analyze sialylated N-linked glycans within biological tissues, providing confident glycan annotations and compositions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Ying Xi, Kevan T. T. Knizner, Kenneth P. P. Garrard, David C. C. Muddiman
Summary: This study presents a mass spectrometry imaging (MSI) method that automatically corrects discernible height differences across surfaces during imaging experiments. A chromatic confocal sensor is incorporated into the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) system to measure the sample surface height at each analytical scan location, allowing for adjustment of the z-axis position of the sample during MSI data acquisition. The method is evaluated using a tilted mouse liver section and an unsectioned Prilosec tablet, showing consistent ablated spot sizes and shapes and revealing the measured ion spatial distribution.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Mary F. Wang, Morgan M. Ritter, Seth W. Kullman, David C. Muddiman
Summary: In this study, the feasibility of sucrose-embedding with paraformaldehyde fixation as an alternative matrix for IR-MALDESI analysis in whole-body zebrafish samples was investigated. The results demonstrated that sucrose-embedding method obtained more lipid annotation information compared to the conventional fresh-frozen sample preparation. This is important for studying and analyzing disease states in whole-body zebrafish.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Juhi Samal, Tana V. Palomino, Judy Chen, David C. Muddiman, Tatiana Segura
Summary: N-linked glycosylation is a complex protein modification that plays a role in cellular signaling and metabolism. Aberrant protein glycosylation is a characteristic feature of many diseases. Spatial profiling of N-glycans through imaging on tissue sections can be used for disease diagnosis. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is a sensitive technique that can be used for mass spectrometry imaging.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Seth M. Eisenberg, Kevan T. Knizner, David C. Muddiman
Summary: Mass spectrometry imaging (MSI) is a technique for measuring and visualizing the spatial distribution of ions in a sample. METASPACE is commonly used for annotation in high-resolution, accurate mass imaging data, but its reported confidence scores often do not accurately reflect the confidence level. The metabolite annotation confidence score (MACS) is an alternative system based on fundamental metrics to generate values that reflect the confidence of an annotation in HRAM-MSI data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Alena N. Joignant, Morgan M. Ritter, Kevan T. Knizner, Kenneth P. Garrard, Seth W. Kullman, David C. Muddiman
Summary: This study proposes a novel method of mass spectrometry imaging (MSI) to reduce the acquisition time of MSI data using nested regions of interest (nROIs). By utilizing nROIs, a smaller region of interest can be imaged at higher spatial resolution nested within a larger region of interest at lower spatial resolution, conserving maximal spatial and chemical information while decreasing acquisition time. The nROI method was characterized on mouse liver and applied to top-hat MSI of zebrafish, resulting in significant improvements in acquisition time and spatial detail. The nROI method can be applied to any method where acquiring larger high-resolution ROIs poses a practical challenge.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)