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Special Issue "Mass Spectrometric Proteomics II"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: 15 January 2021.

Special Issue Editors

Prof. Pierluigi Luigi Mauri
Website
Guest Editor
Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), 20090 Segrate (MI), Italy
Interests: mass spectrometry coupled to mono- and two-dimensional liquid chromatography; MudPIT; clinical proteomics; systems biology; personalized medicine; computational tools for proteomics
Prof. Martina Marchetti-Deschmann
Website
Guest Editor
Institute of Chemical Technologies and Analytics, TU Wien, Austria
Interests: mass spectrometry; MALDI; LC-MS; ion mobility; mass spectrometry imaging; spatial omics; tissue morphology; native mass spectrometry; collision induced dissociation; structure elucidation; protein characterization; proteomics; glycomics; metabolimics; bacterial interactions; skin; cancer; precision medicine
Dr. Diana Canetti
Website SciProfiles
Guest Editor
Centre for Amyloidosis & Acute Phase Proteins, Division of Medicine, University College London,Rowland Hill Street, London NW3 2PF, UK.
Interests: proteomics; mass spectrometry; maldi; lc-ms; amyloid characterization; clinical proteomics; mass spectrometry-based quantification; targeted proteomics; post-translational modifications; protein–protein interaction; protein biochemistry; biomarkers discovery

Special Issue Information

Dear Colleagues,

In the last two decades, the investigation of genome, including transcriptome, has been widely applied and has permitted us to improve our undestanding of it; however, at the same time, it has increased the demand to characterize other -omes sectors, such as proteome and metabolome, in order to find a complete description at molecular level of the biological mechanisms.

In addition, the improvements of both proteomics applications and related hypenated techniques, such as mono- and two-dimensional chromatography coupled to tandem mass spectrometry, have permitted us to develop the so-called mass spectrometry-based proteomics. Today, the MS-based approach has become the gold standard for proteomics study, as it allows the identification of thousands proteins for each analysis and the investigation of a wide range of samples, without limits concerning molecular weight, isoelectric point or hydrophobicity, including protein aggregates.

This Special Issue on “Mass Spectrometric Proteomics” will cover several topics, including but not limited to:

  • Proteome analysis;
  • Study of protein–protein interactions;
  • Clinical proteomics;
  • Proteomics for biomarker discovery;
  • Proteomics for amyloid investigations;
  • Quantitative proteomics by label-free or label-based approaches;
  • Mass spectrometry analysis for the identification and the characterization of post-translational modifications (PTMs);
  • Study of protein structure by mass spectrometry;
  • MS-based proteomics imaging;
  • Development of new analytical MS-based methods.

We warmly invite our colleagues to submit their original contributions to this Special Issue in order to provide recent updates regarding analytical MS-based methods for proteomics that will be of interest to our readers, including o-line separation techniques; native and structural analysis;,such as hydrogen deuterium exchange (HDX); cross-linking and top–down; imaging; data-independent analysis (DIA); protein–protein interactions and single cell analysis; and integration with dedicated computational tools.

We would be delighted if you could respond to confirm your contribution and the proposed title by 30 September 2020 to assist in planning the whole project.

Prof. Pierluigi Mauri
Prof. Martina Marchetti-Deschmann
Dr. Diana Canetti
Guest Editors

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 papers will be 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. Molecules 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 2000 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

  • Proteomics
  • Mass Spectrometry
  • Aggregated proteins/amyloid
  • Native/structural analysis
  • Emergeting DIA and single-cell approaches
  • Targeted proteomics
  • Imaging
  • Top Down
  • Protein–protein interactions
  • Quantitation
  • Biomarkers discovery
  • Post-translational modifications (PTMs)

Published Papers (5 papers)

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Research

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Open AccessArticle
Comparative Proteomic Analysis of Dipsacus asperoides Roots from Different Habitats in China
Molecules 2020, 25(16), 3605; https://doi.org/10.3390/molecules25163605 - 08 Aug 2020
Abstract
Dipsacus asperoides is a kind of Chinese herbal medicine with beneficial health properties. To date, the quality of D. asperoides from different habitats has shown significant differences. However, the molecular differences in D. asperoides from different habitats are still unknown. The aim of [...] Read more.
Dipsacus asperoides is a kind of Chinese herbal medicine with beneficial health properties. To date, the quality of D. asperoides from different habitats has shown significant differences. However, the molecular differences in D. asperoides from different habitats are still unknown. The aim of this study was to investigate the differences in protein levels of D. asperoides from different habitats. Isobaric tags for relative and absolute quantification (iTRAQ) and 2DLC/MS/MS were used to detect statistically significant changes in D. asperoides from different habitats. Through proteomic analysis, a total of 2149 proteins were identified, of which 42 important differentially expressed proteins were screened. Through in-depth analysis of differential proteins, the protein metabolism energy and carbohydrate metabolism of D. asperoides from Hubei Province were strong, but their antioxidant capacity was weak. We found that three proteins, UTP-glucose-1-phosphate uridylyltransferase, allene oxide cyclase, and isopentyl diphosphate isomerase 2, may be the key proteins involved in dipsacus saponin VI synthesis. Eight proteins were found in D. asperoides in response to environmental stress from different habitats. Quantitative real-time PCR analysis confirmed the accuracy and authenticity of the proteomic analysis. The results of this study may provide the basic information for exploring the cause of differences in secondary metabolites in different habitats of D. asperoides and the protein mechanism governing differences in quality. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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Open AccessArticle
Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis
Molecules 2020, 25(16), 3582; https://doi.org/10.3390/molecules25163582 - 06 Aug 2020
Cited by 1
Abstract
The photosynthetic apparatus and metabolic enzymes of cyanobacteria are subject to various controls, such as transcriptional regulation and post-translational modifications, to ensure that the entire cellular system functions optimally. In particular, phosphorylation plays key roles in many cellular controls such as enzyme activity, [...] Read more.
The photosynthetic apparatus and metabolic enzymes of cyanobacteria are subject to various controls, such as transcriptional regulation and post-translational modifications, to ensure that the entire cellular system functions optimally. In particular, phosphorylation plays key roles in many cellular controls such as enzyme activity, signal transduction, and photosynthetic apparatus restructuring. Therefore, elucidating the governing functions of phosphorylation is crucial to understanding the regulatory mechanisms underlying metabolism and photosynthesis. In this study, we determined protein content and phosphorylation levels to reveal the regulation of intracellular metabolism and photosynthesis in Synechocystis sp. PCC 6803; for this, we obtained quantitative data of proteins and their phosphorylated forms involved in photosynthesis and metabolism under various growth conditions (photoautotrophic, mixotrophic, heterotrophic, dark, and nitrogen-deprived conditions) using targeted proteomic and phosphoproteomic analyses with nano-liquid chromatography-triple quadrupole mass spectrometry. The results indicated that in addition to the regulation of protein expression, the regulation of phosphorylation levels of cyanobacterial photosynthetic apparatus and metabolic enzymes was pivotal for adapting to changing environmental conditions. Furthermore, reduced protein levels of CpcC and altered phosphorylation levels of CpcB, ApcA, OCP, and PsbV contributed to the cellular response of the photosynthesis apparatus to nitrogen deficiency. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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Open AccessArticle
Plasma-Based Proteomics Profiling of Patients with Hyperthyroidism after Antithyroid Treatment
Molecules 2020, 25(12), 2831; https://doi.org/10.3390/molecules25122831 - 19 Jun 2020
Abstract
Thyroid hormones critically modulate body homeostasis and haemostasis by regulating energy and metabolism. Previous studies have focused on individual pathways or proteins that are affected by increases in thyroid hormone levels, while an overall plasma proteomic signature of this increased level is lacking. [...] Read more.
Thyroid hormones critically modulate body homeostasis and haemostasis by regulating energy and metabolism. Previous studies have focused on individual pathways or proteins that are affected by increases in thyroid hormone levels, while an overall plasma proteomic signature of this increased level is lacking. Herein, an integrated untargeted proteomic approach with network analysis was used to identify changes in circulating proteins in the plasma proteome between hyperthyroid and euthyroid states. Plasma from 10 age-matched subjects at baseline (hyperthyroid) and post treatment with carbimazole (euthyroid) was compared by difference gel electrophoresis (DIGE) and matrix-assisted laser desorption/ionization time of flight (MALDI TOF) mass spectrometry (MS). A total of 20 proteins were identified with significant difference in abundance (analysis of variance (ANOVA) test, p ≤ 0.05; fold-change ≥ 1.5) between the two states (12 increased and 8 decreased in abundance in the hyperthyroid state). Twelve protein spots corresponding to ten unique proteins were significantly more abundant in the hyperthyroid state compared with the euthyroid state. These increased proteins were haptoglobin (HP), hemopexin (HPX), clusterin (CLU), apolipoprotein L1 (APOL1), alpha-1-B glycoprotein (A1BG), fibrinogen gamma chain (FGG), Ig alpha-1 chain C region (IGHA1), complement C6 (C6), leucine rich alpha 2 glycoprotein (LRG1), and carboxypeptidase N catalytic chain (CPN1). Eight protein spots corresponding to six unique proteins were significantly decreased in abundance in the hyperthyroid samples compared with euthyroid samples. These decreased proteins were apolipoprotein A1 (APOA1), inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), plasminogen (PLG), alpha-1 antitrypsin (SERPINA1), fibrinogen beta chain (FGB), and complement C1r subcomponent (C1R). The differentially abundant proteins were investigated by ingenuity pathway analysis (IPA). The network pathway identified related to infectious disease, inflammatory disease, organismal injury and abnormalities, and the connectivity map focused around two central nodes, namely the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and p38 mitogen-activated protein kinase (MAPK) pathways. The plasma proteome of patients with hyperthyroidism revealed differences in the abundance of proteins involved in acute phase response signaling, and development of a hypercoagulable and hypofibrinolytic state. Our findings enhance our existing knowledge of the altered proteins and associated biochemical pathways in hyperthyroidism. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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Review

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Open AccessReview
Current Status of Matrix-Assisted Laser Desorption/Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in Clinical Diagnostic Microbiology
Molecules 2020, 25(20), 4775; https://doi.org/10.3390/molecules25204775 - 17 Oct 2020
Abstract
Mass spectrometry (MS), a core technology for proteomics and metabolomics, is currently being developed for clinical applications. The identification of microorganisms in clinical samples using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a representative MS-based proteomics application that is relevant to daily [...] Read more.
Mass spectrometry (MS), a core technology for proteomics and metabolomics, is currently being developed for clinical applications. The identification of microorganisms in clinical samples using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a representative MS-based proteomics application that is relevant to daily clinical practice. This technology has the advantages of convenience, speed, and accuracy when compared with conventional biochemical methods. MALDI-TOF MS can shorten the time used for microbial identification by about 1 day in routine workflows. Sample preparation from microbial colonies has been improved, increasing the accuracy and speed of identification. MALDI-TOF MS is also used for testing blood, cerebrospinal fluid, and urine, because it can directly identify the microorganisms in these liquid samples without prior culture or subculture. Thus, MALDI-TOF MS has the potential to improve patient prognosis and decrease the length of hospitalization and is therefore currently considered an essential tool in clinical microbiology. Furthermore, MALDI-TOF MS is currently being combined with other technologies, such as flow cytometry, to expand the scope of clinical applications. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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Open AccessReview
Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction
Molecules 2020, 25(18), 4133; https://doi.org/10.3390/molecules25184133 - 10 Sep 2020
Abstract
Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and [...] Read more.
Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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