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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: 30 May 2024 | Viewed by 4234

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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

Manuscript Submission Information

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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

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

Published Papers (3 papers)

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Research

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 3 | Viewed by 1054

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 1680

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 922

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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