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The Molecular Application of Mass Spectrometry in Health and Disease
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The Molecular Application of Mass Spectrometry in Health and Disease

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: closed (5 June 2023) | Viewed by 15751

Special Issue Editors

Prof. Dr. Uta Ceglarek

E-Mail Website
Guest Editor
Institute for Laboratory Medicine, University of Leipzig Medical Center, 04103 Leipzig, Germany
Interests: obesity; vascular disease; sterol and PUFA metabolism; metabolomics; proteomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Albert Sickmann

E-Mail Website
Guest Editor
Leibniz-Institut für Analytische Wissenschaften − ISAS − e.V., 44139 Dortmund, Germany
Interests: proteomics; protein network of yeast mitochondria and signal transduction in human platlets, to improve analytical techniques

Special Issue Information

Dear Colleagues, 

In recent decades, mass spectrometry has become a key technology for the analysis of biomarkers in body fluids and tissues. There has been an exponential growth in clinical chemistry, pharmacology, and toxicology applications. MS-based proteomics and metabolomics applications help us to understand complex metabolic processes and to identify biomarkers and potential therapeutic targets. Recently developed spatial and single-cell mass spectrometric approaches are currently opening up new possibilities for understanding biological processes in disease and health. In epidemiological and clinical studies, mass spectrometric metabolomics and proteomics applications offer excellent opportunities for better phenotyping. Starting with newborn screening more than 30 years ago, mass spectrometry entered the clinical laboratory in the fields of toxicology, drug monitoring, microbiology, and metabolism.

In the Special Issue entitled “The Molecular Application of Mass Spectrometry in Health and Disease”, we would like to present current technical and application developments in the field of mass spectrometry from single cells to high-throughput routine applications. Perspectives for future developments in laboratory medicine directing to the clinical aim of predictive, preventive, and personalized medicine by mass spectrometry-based metabolomic and proteomic approaches will be addressed.

Prof. Dr. Uta Ceglarek
Prof. Dr. Albert Sickmann
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. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomarkers in body fluids and tissues
  • MS-based proteomics
  • spatial and single-cell mass spectrometric approaches
  • mass spectrometric metabolomics and proteomics applications
  • spectroscopy (IR, Raman, NMR)

Published Papers (7 papers)

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Research

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13 pages, 2846 KiB  
Article
Suspension TRAPping Filter (sTRAP) Sample Preparation for Quantitative Proteomics in the Low µg Input Range Using a Plasmid DNA Micro-Spin Column: Analysis of the Hippocampus from the 5xFAD Alzheimer’s Disease Mouse Model
by Evangelia Thanou, Frank Koopmans, Débora Pita-Illobre, Remco V. Klaassen, Berna Özer, Ioannis Charalampopoulos, August B. Smit and Ka Wan Li
Cells 2023, 12(9), 1242; https://doi.org/10.3390/cells12091242 - 25 Apr 2023
Cited by 2 | Viewed by 2273
Abstract
Suspension TRAPping filter (sTRAP) is an attractive sample preparation method for proteomics studies. The sTRAP protocol uses 5% SDS that maximizes protein solubilization. Proteins are trapped on a borosilicate glass membrane filter, where SDS is subsequently removed from the filter. After trypsin digestion, [...] Read more.
Suspension TRAPping filter (sTRAP) is an attractive sample preparation method for proteomics studies. The sTRAP protocol uses 5% SDS that maximizes protein solubilization. Proteins are trapped on a borosilicate glass membrane filter, where SDS is subsequently removed from the filter. After trypsin digestion, peptides are analyzed directly by LC-MS. Here, we demonstrated the use of a low-cost plasmid DNA micro-spin column for the sTRAP sample preparation of a dilution series of a synapse-enriched sample with a range of 10–0.3 µg. With 120 ng tryptic peptides loaded onto the Evosep LC system coupled to timsTOF Pro 2 mass spectrometer, we identified 5700 protein groups with 4% coefficient of variation (CoV). Comparing other sample preparation protocols, such as the in-gel digestion and the commercial Protifi S-TRAP with the plasmid DNA micro-spin column, the last is superior in both protein and peptide identification numbers and CoV. We applied sTRAP for the analysis of the hippocampal proteome from the 5xFAD mouse model of Alzheimer’s disease and their wildtype littermates, and revealed 121 up- and 54 down-regulated proteins. Protein changes in the mutant mice point to the alteration of processes related to the immune system and Amyloid aggregation, which correlates well with the known major Alzheimer’s-disease-related pathology. Data are available via ProteomeXchange with the identifier PXD041045. Full article
(This article belongs to the Special Issue The Molecular Application of Mass Spectrometry in Health and Disease)
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13 pages, 841 KiB  
Article
Characterization of Non-Cholesterol Sterols in Microglia Cell Membranes Using Targeted Mass Spectrometry
by Ilijana Begcevic Brkovic, Madlen Reinicke, Soroth Chey, Ingo Bechmann and Uta Ceglarek
Cells 2023, 12(7), 974; https://doi.org/10.3390/cells12070974 - 23 Mar 2023
Viewed by 1412
Abstract
Background: Non-cholesterol sterols, as well as plant sterols, cross the blood–brain barrier and, thus, can be incorporated into cell membranes, affecting the cell’s inflammatory response. The aim of our work was to develop an analytical protocol for a quantitative assessment of the sterol [...] Read more.
Background: Non-cholesterol sterols, as well as plant sterols, cross the blood–brain barrier and, thus, can be incorporated into cell membranes, affecting the cell’s inflammatory response. The aim of our work was to develop an analytical protocol for a quantitative assessment of the sterol composition within the membrane microdomains of microglia. Methods: A protocol for cell membrane isolation using OptiPrepTM gradient ultracentrifugation, in combination with a targeted mass spectrometry (LC-MS/MS)-based assay, was developed and validated for the quantitative analysis of free sterols in microglia cell membranes. Results: Utilizing an established LC-MS/MS assay, cholesterol and seven non-cholesterol sterols were analyzed with a limit of detection from 0.001 to 0.05 mg/L. Applying the detergent-free isolation of SIM-A9 microglia cell membranes, cholesterol (CH), desmosterol (DE), lanosterol (LA) stigmasterol (ST), beta-sitosterol (SI) and campesterol (CA) were quantified with coefficients of variations between 6 and 29% (fractions 4–6, n = 5). The highest concentrations of non-CH sterols within the microglia plasma membranes were found in the microdomain region (DE>LA>SI>ST>CA), with ratios to CH ranging from 2.3 to 435 lower abundancies. Conclusion: By applying our newly developed and validated analytical protocol, we show that the non-CH sterol concentration is about 38% of the total sterol content in microglia membrane microdomains. Further investigations must clarify how changes in the non-sterol composition influence membrane fluidity and cell signaling. Full article
(This article belongs to the Special Issue The Molecular Application of Mass Spectrometry in Health and Disease)
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16 pages, 3105 KiB  
Article
Stability and Requirement for Thiamin in a Cell Culture Feed Used to Produce New Biological Entities
by Alisa Schnellbächer and Aline Zimmer
Cells 2023, 12(2), 334; https://doi.org/10.3390/cells12020334 - 16 Jan 2023
Viewed by 1711
Abstract
Thiamin is susceptible to heat and oxidation, which is a concern for the development of concentrated and room temperature stable feeds used to produce recombinant proteins. Hence, it is critical to understand the reactivity and necessity of the vitamin in liquid feeds to [...] Read more.
Thiamin is susceptible to heat and oxidation, which is a concern for the development of concentrated and room temperature stable feeds used to produce recombinant proteins. Hence, it is critical to understand the reactivity and necessity of the vitamin in liquid feeds to be able to either develop mitigation strategies to stabilize the vitamin or to remove thiamin from formulations if it is unnecessary. LC-MS/MS was used to investigate thiamin stability in different liquid feed formulations and to identify thiamin degradation products. Results indicate oxidation of thiamin and interaction with amino acids, keto acids, and sulfur containing components. Thiamin necessity in feed was assessed during a fed batch experiment, focusing on cell performance and critical quality attributes of the produced recombinant proteins. The impact of thiamin depletion in the feed on the intra- and extracellular metabolome was investigated using untargeted LC-MS/MS. Results indicate that thiamin can be removed from the feed without affecting the performance or the intra- and extracellular metabolome of the tested cell lines. Overall, profound insights on thiamin reactivity and necessity are presented in this study, suggesting the removal of the dispensable and instable vitamin as a simple means for the development of next generation feeds used to produce therapeutic biological entities. Full article
(This article belongs to the Special Issue The Molecular Application of Mass Spectrometry in Health and Disease)
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9 pages, 1371 KiB  
Communication
Non-Steroidal Drug Interferences in a Quantitative Multisteroid LC-MS/MS Assay
by Valentin Braun, Hermann Stuppner and Christoph Seger
Cells 2023, 12(2), 329; https://doi.org/10.3390/cells12020329 - 15 Jan 2023
Cited by 1 | Viewed by 1423
Abstract
Screening for possible interferences from steroidal compounds other than the target analytes (endogenous or exogenous) is well established in LC-MS/MS assay development for steroid quantification in a routine clinical setting. However, interferences from non-steroidal substances have, hitherto, not been explored. After screening more [...] Read more.
Screening for possible interferences from steroidal compounds other than the target analytes (endogenous or exogenous) is well established in LC-MS/MS assay development for steroid quantification in a routine clinical setting. However, interferences from non-steroidal substances have, hitherto, not been explored. After screening more than 150 pharmaceuticals and their metabolites by analyzing commercial quality control samples from TDM analysis kits (Recipe, Chromsystems) with a multisteroid LC-MS/MS assay (protein precipitation followed by HybridSPE filtration, biphenyl column, methanol–water gradient with NH4F additive), we can report the finding of two newly discovered potential interferences from non-steroidal drugs. Antidepressant paroxetine (PX) was identified as an interference to 17-hydroxyprogesterone (17P), and α-hydroxytriazolam (α-OH-TZM)—a major metabolite of benzodiazepine triazolam (TZM)—was identified as an interference to aldosterone (ALDO). Despite different elemental and structural compositions and nominal masses, the M+1 isotopologues of PX and α-OH-TZM produced overlapping signals in ion traces monitored for the respective analytes (m/z 331 → 109/97 and 361→315/343, respectively). PX and TZM are frequently prescribed drugs, and their therapeutic ranges are far exceeding the reference ranges of 17P or ALDO (µmol vs nmol); therefore, these interferences should be considered clinically relevant. Striving for faster multi-analyte methods with high sample turnover, especially in the field of steroid quantification, can limit assay selectivity and specificity. Therefore, supported by the findings of this study, screening for potential interferences in multi-analyte LC-MS/MS method development should not cover only substances of the same class but also include a set of common drugs. Full article
(This article belongs to the Special Issue The Molecular Application of Mass Spectrometry in Health and Disease)
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21 pages, 2522 KiB  
Article
Nuclear Proteomics of Induced Leukemia Cell Differentiation
by Svetlana Novikova, Tatiana Tolstova, Leonid Kurbatov, Tatiana Farafonova, Olga Tikhonova, Natalia Soloveva, Alexander Rusanov, Alexander Archakov and Victor Zgoda
Cells 2022, 11(20), 3221; https://doi.org/10.3390/cells11203221 - 14 Oct 2022
Cited by 6 | Viewed by 2316
Abstract
Studies of induced granulocytic differentiation help to reveal molecular mechanisms of cell maturation. The nuclear proteome represents a rich source of regulatory molecules, including transcription factors (TFs). It is important to have an understanding of molecular perturbations at the early stages of the [...] Read more.
Studies of induced granulocytic differentiation help to reveal molecular mechanisms of cell maturation. The nuclear proteome represents a rich source of regulatory molecules, including transcription factors (TFs). It is important to have an understanding of molecular perturbations at the early stages of the differentiation processes. By applying the proteomic quantitative profiling using isobaric labeling, we found that the contents of 214, 319, 376, 426, and 391 proteins were altered at 3, 6, 9, 12, and 72 h, respectively, compared to 0 h in the HL-60 cell nuclear fraction under all-trans-retinoid acid (ATRA) treatment. From 1860 identified nuclear proteins, 231 proteins were annotated as proteins with transcription factor (TF) activity. Six TFs (RREB1, SRCAP, CCDC124, TRIM24, BRD7, and BUD31) were downregulated and three TFs EWSR1, ENO1, and FUS were upregulated at early time points (3–12 h) after ATRA treatment. Bioinformatic annotation indicates involvement of the HL-60 nuclear proteome in DNA damage recognition in the RUNX1-triggered pathway, and in the p53-regulation pathway. By applying scheduled multiple reaction monitoring using stable isotopically labeled peptide standards (MRM/SIS), we found a persistent increase in the content of the following proteins: PRAM1, CEPBP, RBPJ, and HIC1 in the HL-60 cell nuclear fraction during ATRA-induced granulocytic differentiation. In the case of STAT1, CASP3, PARP1, and PRKDC proteins, a transient increase in their content was observed at early time points (3–12 h) after the ATRA treatment. Obtained data on nuclear proteome composition and dynamics during granulocytic differentiation could be beneficial for the development of new treatment approaches for leukemias with the mutated p53 gene. Full article
(This article belongs to the Special Issue The Molecular Application of Mass Spectrometry in Health and Disease)
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Review

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18 pages, 1858 KiB  
Review
Blood-Derived Lipid and Metabolite Biomarkers in Cardiovascular Research from Clinical Studies: A Recent Update
by Dipali Kale, Amol Fatangare, Prasad Phapale and Albert Sickmann
Cells 2023, 12(24), 2796; https://doi.org/10.3390/cells12242796 - 08 Dec 2023
Cited by 1 | Viewed by 1215
Abstract
The primary prevention, early detection, and treatment of cardiovascular disease (CVD) have been long-standing scientific research goals worldwide. In the past decades, traditional blood lipid profiles have been routinely used in clinical practice to estimate the risk of CVDs such as atherosclerotic cardiovascular [...] Read more.
The primary prevention, early detection, and treatment of cardiovascular disease (CVD) have been long-standing scientific research goals worldwide. In the past decades, traditional blood lipid profiles have been routinely used in clinical practice to estimate the risk of CVDs such as atherosclerotic cardiovascular disease (ASCVD) and as treatment targets for the primary prevention of adverse cardiac events. These blood lipid panel tests often fail to fully predict all CVD risks and thus need to be improved. A comprehensive analysis of molecular species of lipids and metabolites (defined as lipidomics and metabolomics, respectively) can provide molecular insights into the pathophysiology of the disease and could serve as diagnostic and prognostic indicators of disease. Mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based lipidomics and metabolomics analysis have been increasingly used to study the metabolic changes that occur during CVD pathogenesis. In this review, we provide an overview of various MS-based platforms and approaches that are commonly used in lipidomics and metabolomics workflows. This review summarizes the lipids and metabolites in human plasma/serum that have recently (from 2018 to December 2022) been identified as promising CVD biomarkers. In addition, this review describes the potential pathophysiological mechanisms associated with candidate CVD biomarkers. Future studies focused on these potential biomarkers and pathways will provide mechanistic clues of CVD pathogenesis and thus help with the risk assessment, diagnosis, and treatment of CVD. Full article
(This article belongs to the Special Issue The Molecular Application of Mass Spectrometry in Health and Disease)
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23 pages, 3048 KiB  
Review
MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology
by Maureen Feucherolles and Gilles Frache
Cells 2022, 11(23), 3900; https://doi.org/10.3390/cells11233900 - 02 Dec 2022
Cited by 11 | Viewed by 4239
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in [...] Read more.
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories. Full article
(This article belongs to the Special Issue The Molecular Application of Mass Spectrometry in Health and Disease)
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