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High Resolution Mass Spectrometry in Molecular Sciences: 2nd Edition
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High Resolution Mass Spectrometry in Molecular Sciences: 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (20 May 2025) | Viewed by 5918

Special Issue Editor

Prof. Dr. Laszlo Prokai

E-Mail Website
Guest Editor
Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA
Interests: chemical neuroscience; CNS drug discovery; neurobiochemistry of estrogens; biomedical mass spectrometry; chemical proteomics; omics-driven research in molecular sciences
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Special Issue Information

Dear Colleagues,

An aspiration for high resolution, accuracy and sensitivity in spectroscopic and spectrometric methods can be paraphrased by the old Olympic motto of Citius, Altius, Fortius (faster, higher, stronger). Demands for high mass-resolving power and mass measurement accuracy, as well as speedy data acquisition, have been the driving forces toward advances in instrumentation that facilitate the pursuit of challenging applications of mass spectrometry. The introduction of the Fourier transform (FT) approach, development of the high-resolution time-of-flight (TOF) and ion mobility (IM) methods of ion sorting have propelled a paradigm shift to meet these challenges. FT ion cyclotron resonance (FT-ICR), OrbitrapTM and TOF instruments are commercially available in many of today’s mass spectrometers and often in “hybrid” configurations that bring them together seamlessly with other analyzers such as quadrupoles, ion traps and IM spectrometry within one instrument. They now deliver superior performance to the delight of the broad scientific community. In addition to conventional research articles and reviews, this Special Issue (expanded in breadth from an earlier series of IJMS articles devoted to high-resolution mass spectrometry in molecular sciences) also welcomes commentaries, opinions and perspectives on the progress and applications of high-resolution mass spectrometry in broad areas of molecular sciences.

Prof. Dr. Laszlo Prokai
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • antibodies
  • astrobiology
  • biomarkers
  • drug discovery
  • drug development
  • drug metabolism
  • Fourier transform
  • glycomics
  • imaging
  • ion cyclotron resonance
  • ion mobility
  • lipids
  • lipidomics
  • mass spectrometry
  • metabolomics
  • nucleic acids
  • Orbitrap
  • organometallics
  • polymers
  • peptides
  • proteins
  • proteomics
  • structural biology
  • structure elucidation
  • tandem mass spectrometry
  • time-of-flight

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Related Special Issue

Published Papers (3 papers)

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Research

22 pages, 12201 KiB  
Article
Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics
by Gergő Kalló, Khadiza Zaman, László Potor, Zoltán Hendrik, Gábor Méhes, Csaba Tóth, Péter Gergely, József Tőzsér, György Balla, József Balla, Laszlo Prokai and Éva Csősz
Int. J. Mol. Sci. 2024, 25(24), 13665; https://doi.org/10.3390/ijms252413665 - 20 Dec 2024
Viewed by 1268
Abstract
Vulnerable atherosclerotic plaques, especially hemorrhaged lesions, are the major cause of mortalities related to vascular pathologies. The early identification of vulnerable plaques helps to stratify patients at risk of developing acute vascular events. In this study, proteomics analyses of human carotid artery samples [...] Read more.
Vulnerable atherosclerotic plaques, especially hemorrhaged lesions, are the major cause of mortalities related to vascular pathologies. The early identification of vulnerable plaques helps to stratify patients at risk of developing acute vascular events. In this study, proteomics analyses of human carotid artery samples collected from patients with atheromatous plaques and complicated lesions, respectively, as well as from healthy controls were performed. The proteins isolated from the carotid artery samples were analyzed by a bottom-up shotgun approach that relied on nanoflow liquid chromatography–tandem mass spectrometry analyses (LC–MS/MS) using both data-dependent (DDA) and data-independent (DIA) acquisitions. The data obtained by high-resolution DIA analyses displayed a stronger distinction among groups compared to DDA analyses. Differentially expressed proteins were further examined using Ingenuity Pathway Analysis® with focus on pathological and molecular processes driving atherosclerosis. From the more than 150 significantly regulated canonical pathways, atherosclerosis signaling and neutrophil extracellular trap signaling were verified by protein-targeted data extraction. The results of our study are expected to facilitate a better understanding of the disease progression’s molecular drivers and provide inspiration for further multiomics and hypothesis-driven studies. Full article
(This article belongs to the Special Issue High Resolution Mass Spectrometry in Molecular Sciences: 2nd Edition)
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11 pages, 4104 KiB  
Article
Applying UHPLC-HRAM MS/MS Method to Assess Host Cell Protein Clearance during the Purification Process Development of Therapeutic mAbs
by Reiko Kiyonami, Rafael Melani, Ying Chen, AI De Leon and Min Du
Int. J. Mol. Sci. 2024, 25(17), 9687; https://doi.org/10.3390/ijms25179687 - 7 Sep 2024
Viewed by 1398
Abstract
Host cell proteins (HCPs) are one of the process-related impurities that need to be well characterized and controlled throughout biomanufacturing processes to assure the quality, safety, and efficacy of monoclonal antibodies (mAbs) and other protein-based biopharmaceuticals. Although ELISA remains the gold standard method [...] Read more.
Host cell proteins (HCPs) are one of the process-related impurities that need to be well characterized and controlled throughout biomanufacturing processes to assure the quality, safety, and efficacy of monoclonal antibodies (mAbs) and other protein-based biopharmaceuticals. Although ELISA remains the gold standard method for quantification of total HCPs, it lacks the specificity and coverage to identify and quantify individual HCPs. As a complementary method to ELISA, the LC-MS/MS method has emerged as a powerful tool to identify and profile individual HCPs during the downstream purification process. In this study, we developed a sensitive, robust, and reproducible analytical flow ultra-high-pressure LC (UHPLC)-high-resolution accurate mass (HRAM) data-dependent MS/MS method for HCP identification and monitoring using an Orbitrap Ascend BioPharma Tribrid mass spectrometer. As a case study, the developed method was applied to an in-house trastuzumab product to assess HCP clearance efficiency of the newly introduced POROS™ Caprylate Mixed-Mode Cation Exchange Chromatography resin (POROS Caprylate mixed-mode resin) by monitoring individual HCP changes between the trastuzumab sample collected from the Protein A pool (purified by Protein A chromatography) and polish pool (purified by Protein A first and then further purified by POROS Caprylate mixed-mode resin). The new method successfully identified the total number of individual HCPs in both samples and quantified the abundance changes in the remaining HCPs in the polish purification sample. Full article
(This article belongs to the Special Issue High Resolution Mass Spectrometry in Molecular Sciences: 2nd Edition)
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12 pages, 3093 KiB  
Article
A Mass Spectrometry Strategy for Protein Quantification Based on the Differential Alkylation of Cysteines Using Iodoacetamide and Acrylamide
by Dávid Virág, Gitta Schlosser, Adina Borbély, Gabriella Gellén, Dávid Papp, Zoltán Kaleta, Borbála Dalmadi-Kiss, István Antal and Krisztina Ludányi
Int. J. Mol. Sci. 2024, 25(9), 4656; https://doi.org/10.3390/ijms25094656 - 25 Apr 2024
Viewed by 2290
Abstract
Mass spectrometry has become the most prominent yet evolving technology in quantitative proteomics. Today, a number of label-free and label-based approaches are available for the relative and absolute quantification of proteins and peptides. However, the label-based methods rely solely on the employment of [...] Read more.
Mass spectrometry has become the most prominent yet evolving technology in quantitative proteomics. Today, a number of label-free and label-based approaches are available for the relative and absolute quantification of proteins and peptides. However, the label-based methods rely solely on the employment of stable isotopes, which are expensive and often limited in availability. Here we propose a label-based quantification strategy, where the mass difference is identified by the differential alkylation of cysteines using iodoacetamide and acrylamide. The alkylation reactions were performed under identical experimental conditions; therefore, the method can be easily integrated into standard proteomic workflows. Using high-resolution mass spectrometry, the feasibility of this approach was assessed with a set of tryptic peptides of human serum albumin. Several critical questions, such as the efficiency of labeling and the effect of the differential alkylation on the peptide retention and fragmentation, were addressed. The concentration of the quality control samples calculated against the calibration curves were within the ±20% acceptance range. It was also demonstrated that heavy labeled peptides exhibit a similar extraction recovery and matrix effect to light ones. Consequently, the approach presented here may be a viable and cost-effective alternative of stable isotope labeling strategies for the quantification of cysteine-containing proteins. Full article
(This article belongs to the Special Issue High Resolution Mass Spectrometry in Molecular Sciences: 2nd Edition)
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