Review
Biochemical Research Methods
Yi Yang, Liang Qiao
Summary: Protein post-translational modifications (PTMs) increase the functional diversity of the cellular proteome. Accurate quantification and identification of protein PTMs is crucial in proteomics research. Recent advancements in data-independent acquisition (DIA) mass spectrometry (MS) have enabled deep coverage and accurate quantification of PTMs. This review provides an overview of DIA data processing methods for PTMs analysis, as well as deep learning methods that enhance PTMs analysis. The limitations and future directions of DIA methods for PTMs analysis are also discussed.
Article
Biochemical Research Methods
Yuxuan Liao, Miao Tian, Hailiang Zhang, Hongmei Lu, Yonglei Jiang, Yi Chen, Zhimin Zhang
Summary: This study developed a deep learning-based method called DeepPIC for feature extraction from LC-MS datasets. DeepPIC uses a customized U-Net model to directly and automatically find pure ion chromatograms (PICs) from centroid mode data of LC-MS. The results showed that DeepPIC outperforms traditional methods in recall rates and correlation with sample concentrations, making it an automatic, practical, and off-the-shelf method for feature extraction.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Health Care Sciences & Services
Xinyan Zhang, Nengjun Yi
Summary: The article introduces zero-inflated models for analyzing microbiome abundance data and proposes a Bayesian predictive value approach (BPV) to estimate the overall effect of microbiome abundance. Simulation and real data applications demonstrate the superiority of the proposed approach, especially in cases with small sample size and high zero-inflation rate.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2022)
Article
Biochemical Research Methods
Sujun Li, Jianhui Zhu, David M. Lubman, He Zhou, Haixu Tang
Summary: Liquid chromatography coupled with tandem mass spectrometry is commonly used in large-scale glycoproteomic studies. A novel concurrent approach for glycopeptide identification in multiple related data sets is presented using spectral clustering and spectral library searching. Evaluation on two large-scale data sets showed that this approach can identify 105%-224% more spectra as glycopeptides compared to using Byonic alone, enabling the discovery of potential biomarkers in hepatocellular carcinoma.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Public, Environmental & Occupational Health
Dinesh Kumar Barupal, Sadjad Fakouri Baygi, Robert O. Wright, Manish Arora
Summary: Untargeted chemical analysis of bio-fluids provides semi-quantitative data for thousands of chemicals, but commonly used stringent signal thresholds may lead to missing important biological insights. Re-analyzing data with minimum possible thresholds revealed metabolic insights that were previously missed, suggesting that data processing thresholds should be used at minimal levels or completely avoided for mining untargeted chemical analysis data in exposome research.
FRONTIERS IN PUBLIC HEALTH
(2021)
Article
Pharmacology & Pharmacy
Shreedhar S. Otari, Suraj B. Patel, Manoj M. Lekhak, Savaliram G. Ghane
Summary: This research investigated the phytochemical profile and bioactivities of Barleria terminalis and Calacanthus grandiflorus. The results showed the presence of phenolic compounds and phenylethanoid glycosides in these plants. Additionally, they exhibited potential antioxidant, enzyme inhibitory, and anti-diabetic activities. These findings provide a basis for further research and utilization of these plants.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemical Research Methods
Kirsten E. E. Overdahl, Justin B. B. Collier, Anton M. M. Jetten, Alan K. K. Jarmusch
Summary: Feature finding is a common method in processing untargeted mass spectrometry data to obtain a list of chemicals present in a sample. This study introduces signal response evaluation as a method to assess the individual features observed in untargeted MS data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Sam Wouters, Sebastiaan Eeltink, Rob Haselberg, Govert W. Somsen, Andrea F. G. Gargano
Summary: A membrane-based microfluidic chip was developed for selective post-column removal of TFA anions from HILIC, improving ionization and reducing TFA adduct formation. The device's multichannel design allows the use of 0.1% TFA mobile phases while maintaining separation selectivity and efficiency.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Martina Pirro, Yassene Mohammed, Arnoud H. de Ru, George M. C. Janssen, Rayman T. N. Tjokrodirijo, Katarina Madunic, Manfred Wuhrer, Peter A. van Veelen, Paul J. Hensbergen
Summary: Developments in mass spectrometry (MS)-based analyses of glycoproteins have been crucial in studying glycosylation changes related to diseases. The characteristic pattern of oxonium ions in glycopeptide fragmentation spectra can help assign different sets of glycopeptides, particularly distinguishing between O-GalNAc and O-GlcNAc. By analyzing the relative intensities of oxonium ions, accurate assignment of glycopeptides can be achieved even in complex proteomics datasets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Carlos Perez-Lopez, Bernat Oro-Noll, Silvia Lacorte, Roma Tauler
Summary: New data-independent acquisition (DIA) modes coupled to chromatographic separations are revolutionizing the processing of mass spectrometric (MS) data using chemometric methods. In this study, the authors demonstrate the application of the regions of interest multivariate curve resolution (ROIMCR) method for the simultaneous analysis of MS1 and MS2 DIA raw data. The ROIMCR method allows for fast direct resolution of elution and spectral profiles without the need for peak matching, alignment, or modeling.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
Summary: This study introduces a new storage format called mzMD for MS datasets and presents an algorithm to query this format for summarizing a given data window. Experimental results demonstrate the high speed and stability of mzMD in retrieving high-quality data window summaries.
Article
Automation & Control Systems
Youngjae Oh, Shinjune Kim, Seongho Kim, Jaesik Jeong
Summary: This article presents a metabolite identification software in the form of R Shiny, which can be used for metabolite identification in gas chromatography-mass spectrometry (GC-MS)-based untargeted metabolomics. The software provides various similarity measures and a toy example using a graphical user interface.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2023)
Article
Chemistry, Medicinal
Araceli E. Rossignoli, Carmen Marino, Helena Martin, Juan Blanco
Summary: GYM D and 16-desmethyl GYM D, along with two tetrodotoxin analogues, were discovered in invertebrates from the north Atlantic coast of Spain between May 2021 and October 2022. This is the first report of GYM D and 16-desmethyl GYM D in invertebrates worldwide, as well as the first identification of the tetrodotoxin analogues in the north Atlantic coast of Spain. Tetrodotoxin (TTX) was also detected for the first time in three species, highlighting the importance of analyzing toxin analogues and metabolites for effective monitoring programs and health protection.
Article
Biochemistry & Molecular Biology
Hassan Shikshaky, Eman Abdelnaby Ahmed, Ali Mostafa Anwar, Aya Osama, Shahd Ezzeldin, Antony Nasr, Sebaey Mahgoub, Sameh Magdeldin
Summary: This article aims to develop a novel SWATH platform for metabolite identification using accurate mass spectral library, providing new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Laura S. Bailey, Fanran Huang, Tianqi Gao, Jinying Zhao, Kari B. Basso, Zhongwu Guo
Summary: A new strategy for GSL characterization and glycolipidomics analysis was developed based on two-stage matching of experimental and reference MS/MS spectra. This method uses the whole spectrum for GSL characterization, and is expected to accelerate glycolipidomics analysis and reveal new and diverse lipid forms of GSLs.
ANALYTICAL CHEMISTRY
(2021)
