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

Deadline for manuscript submissions: 20 October 2024 | Viewed by 5928

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Dr. Dragan Nikolic

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Guest Editor

Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
Interests: quadrupole ion trap mass spectroscopy; atomic and molecular physics; plasma spectroscopy; protein–ligand interactions; dissipative particle dynamics

Special Issue Information

Dear Colleagues,

Modern applications of mass spectrometry techniques in molecular and structural biology rely on the ability to vaporize and ionize macromolecules, which was made possible with the advent of electrospray ionization coupled to liquid chromatography or matrix-assisted laser desorption/ionization coupled to high-resolution mass spectrometers. Quantitative studies of individual macromolecules and their function in cells grown in different media were made possible by isotope-coded affinity tags technology. With the ever-growing volume of biological molecules' mass spectra data, our ability to identify them in complex mixtures relies on the continuous development of efficient algorithms to search, rank, and interpret entries in online databases. This Special Issue on "Mass Spectrometry in Molecular Biology" invites original research and reviews on all aspects of development, verification, and maturation of sample preparation protocols, measurement techniques, and supporting computational and theoretical methods to interpret the structural and functional properties of biomolecules.

Dr. Dragan Nikolic
Guest Editor

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Keywords

mass spectrometry of biomolecules
native/modified peptides, proteins, lipids, and metabolites
sample preparation, extraction, and ionization techniques
ion fragmentation pattern recognition
statistical analysis of identification results

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Published Papers (4 papers)

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Research

19 pages, 5500 KiB

Open AccessArticle

Characterisation of Canine and Feline Breast Tumours, Their Metastases, and Corresponding Primary Cell Lines Using LA-REIMS and DESI-MS Imaging

by Adrienn Molnár, Gabriel Stefan Horkovics-Kováts, Nóra Kucsma, Zsuzsanna Szegő, Boglárka Tauber, Attila Egri, Zoltán Szkupien, Bálint András Deák, James S. McKenzie, Julianna Thuróczy, Richard Schäffer, Gitta Schlosser, Gergely Szakács and Júlia Balog

Int. J. Mol. Sci. 2024, 25(14), 7752; https://doi.org/10.3390/ijms25147752 - 15 Jul 2024

Viewed by 571

Abstract

Breast cancer, a complex disease with a significant prevalence to form metastases, necessitates novel therapeutic strategies to improve treatment outcomes. Here, we present the results of a comparative molecular study of primary breast tumours, their metastases, and the corresponding primary cell lines using Desorption Electrospray Ionisation (DESI) and Laser-Assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) imaging. Our results show that ambient ionisation mass spectrometry technology is suitable for rapid characterisation of samples, providing a lipid- and metabolite-rich spectrum within seconds. Our study demonstrates that the lipidomic fingerprint of the primary tumour is not significantly distinguishable from that of its metastasis, in parallel with the similarity observed between their respective primary cell lines. While significant differences were observed between tumours and the corresponding cell lines, distinct lipidomic signatures and several phospholipids such as PA(36:2), PE(36:1), and PE(P-38:4)/PE(O-38:5) for LA-REIMS imaging and PE(P-38:4)/PE(O-38:5), PS(36:1), and PI(38:4) for DESI-MSI were identified in both tumours and cells. We show that the tumours’ characteristics can be found in the corresponding primary cell lines, offering a promising avenue for assessing tumour responsiveness to therapeutic interventions. A comparative analysis by DESI-MSI and LA-REIMS imaging revealed complementary information, demonstrating the utility of LA-REIMS in the molecular imaging of cancer. Full article

(This article belongs to the Special Issue Mass Spectrometry in Molecular Biology)

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19 pages, 1665 KiB

Open AccessArticle

Molecular Identification and Acid Stress Response of an Acidithiobacillus thiooxidans Strain Isolated from Rio Tinto (Spain)

by Ana Ibáñez, Carlos Barreiro, Alba Diez-Galán, Rebeca Cobos, Carla Calvo-Peña and Juan José R. Coque

Int. J. Mol. Sci. 2023, 24(17), 13391; https://doi.org/10.3390/ijms241713391 - 29 Aug 2023

Cited by 4 | Viewed by 1363

Abstract

Acidithiobacillus thiooxidans is of paramount importance in the development of biomining technologies. Being widely recognized as an extreme acidophile, extensive research has been dedicated to understanding its significant role in the extraction of several ores in recent years. However, there still exist significant molecular uncertainties surrounding this species. This study focuses on developing a taxonomic assignment method based on the sequencing of the 16S-5S rRNA cluster, along with a qPCR-based technology enabling precise growth determination. Additionally, an approach to understanding its response to acid stress is explored through RT-PCR and MALDI-TOF analysis. Our findings indicate that when subjected to pH levels below 1, the cell inhibits central (carbon fixation and metabolism) and energy (sulfur metabolism) metabolism, as well as chaperone synthesis, suggesting a potential cellular collapse. Nevertheless, the secretion of ammonia is enhanced to raise the environmental pH, while fatty acid synthesis is upregulated to reinforce the cell membrane. Full article

(This article belongs to the Special Issue Mass Spectrometry in Molecular Biology)

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14 pages, 3421 KiB

Open AccessArticle

Detection and Monitoring of Tumor-Derived Mutations in Circulating Tumor DNA Using the UltraSEEK Lung Panel on the MassARRAY System in Metastatic Non-Small Cell Lung Cancer Patients

by Paul van der Leest, Melanie Janning, Naomi Rifaela, Maria L. Aguirre Azpurua, Jolanthe Kropidlowski, Sonja Loges, Nicolas Lozano, Alexander Sartori, Darryl Irwin, Pierre-Jean Lamy, T. Jeroen N. Hiltermann, Harry J. M. Groen, Klaus Pantel, Léon C. van Kempen, Harriet Wikman and Ed Schuuring

Int. J. Mol. Sci. 2023, 24(17), 13390; https://doi.org/10.3390/ijms241713390 - 29 Aug 2023

Cited by 2 | Viewed by 2095

Abstract

Analysis of circulating tumor DNA (ctDNA) is a potential minimally invasive molecular tool to guide treatment decision-making and disease monitoring. A suitable diagnostic-grade platform is required for the detection of tumor-specific mutations with high sensitivity in the circulating cell-free DNA (ccfDNA) of cancer patients. In this multicenter study, the ccfDNA of 72 patients treated for advanced-stage non-small cell lung cancer (NSCLC) was evaluated using the UltraSEEK^® Lung Panel on the MassARRAY^® System, covering 73 hotspot mutations in EGFR, KRAS, BRAF, ERBB2, and PIK3CA against mutation-specific droplet digital PCR (ddPCR) and routine tumor tissue NGS. Variant detection accuracy at primary diagnosis and during disease progression, and ctDNA dynamics as a marker of treatment efficacy, were analyzed. A multicenter evaluation using reference material demonstrated an overall detection rate of over 90% for variant allele frequencies (VAFs) > 0.5%, irrespective of ccfDNA input. A comparison of UltraSEEK^® and ddPCR analyses revealed a 90% concordance. An 80% concordance between therapeutically targetable mutations detected in tumor tissue NGS and ccfDNA UltraSEEK^® analysis at baseline was observed. Nine of 84 (11%) tumor tissue mutations were not covered by UltraSEEK^®. A decrease in ctDNA levels at 4–6 weeks after treatment initiation detected with UltraSEEK^® correlated with prolonged median PFS (46 vs. 6 weeks; p < 0.05) and OS (145 vs. 30 weeks; p < 0.01). Using plasma-derived ccfDNA, the UltraSEEK^® Lung Panel with a mid-density set of the most common predictive markers for NSCLC is an alternative tool to detect mutations both at diagnosis and during disease progression and to monitor treatment response. Full article

(This article belongs to the Special Issue Mass Spectrometry in Molecular Biology)

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13 pages, 1730 KiB

Open AccessArticle

Global Protein Profiling in Processed Immunohistochemistry Tissue Sections

by Simone Venz, Viola von Bohlen und Halbach, Christian Hentschker, Heike Junker, Andreas Walter Kuss, Thomas Sura, Elke Krüger, Uwe Völker, Oliver von Bohlen und Halbach, Lars Riff Jensen and Elke Hammer

Int. J. Mol. Sci. 2023, 24(14), 11308; https://doi.org/10.3390/ijms241411308 - 11 Jul 2023

Viewed by 1167

Abstract

Tissue sections, which are widely used in research and diagnostic laboratories and have already been examined by immunohistochemistry (IHC), may subsequently provide a resource for proteomic studies, even though only small amount of protein is available. Therefore, we established a workflow for tandem mass spectrometry-based protein profiling of IHC specimens and characterized defined brain area sections. We investigated the CA1 region of the hippocampus dissected from brain slices of adult C57BL/6J mice. The workflow contains detailed information on sample preparation from brain slices, including removal of antibodies and cover matrices, dissection of region(s) of interest, protein extraction and digestion, mass spectrometry measurement, and data analysis. The Gene Ontology (GO) knowledge base was used for further annotation. Literature searches and Gene Ontology annotation of the detected proteins verify the applicability of this method for global protein profiling using formalin-fixed and embedded material and previously used IHC slides. Full article

(This article belongs to the Special Issue Mass Spectrometry in Molecular Biology)

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