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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: closed (15 January 2021) | Viewed by 35750

Special Issue Editors


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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
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Institute of Chemical Technologies and Analytics, TU Wien, 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

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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 Issues, Collections and Topics in MDPI journals

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 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. 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 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

  • 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 (11 papers)

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Research

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24 pages, 6504 KiB  
Article
Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status
by Jasmin Dülfer, Hao Yan, Maxim N. Brodmerkel, Robert Creutznacher, Alvaro Mallagaray, Thomas Peters, Carl Caleman, Erik G. Marklund and Charlotte Uetrecht
Molecules 2021, 26(8), 2125; https://doi.org/10.3390/molecules26082125 - 07 Apr 2021
Cited by 10 | Viewed by 3162
Abstract
Noroviruses are the major cause of viral gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens [...] Read more.
Noroviruses are the major cause of viral gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens (HBGAs) in a strain-dependent manner but how these glycan-interactions actually relate to cell entry remains unclear. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) is used to investigate glycan-induced protein dynamics in P dimers of different strains, which exhibit high structural similarity but different prevalence in humans. While the almost identical strains GII.4 Saga and GII.4 MI001 share glycan-induced dynamics, the dynamics differ in the emerging GII.17 Kawasaki 308 and rare GII.10 Vietnam 026 strain. The structural aspects of glycan binding to fully deamidated GII.4 P dimers have been investigated before. However, considering the high specificity and half-life of N373D under physiological conditions, large fractions of partially deamidated virions with potentially altered dynamics in their P domains are likely to occur. Therefore, we also examined glycan binding to partially deamidated GII.4 Saga and GII.4 MI001 P dimers. Such mixed species exhibit increased exposure to solvent in the P dimer upon glycan binding as opposed to pure wildtype. Furthermore, deamidated P dimers display increased flexibility and a monomeric subpopulation. Our results indicate that glycan binding induces strain-dependent structural dynamics, which are further altered by N373 deamidation, and hence hint at a complex role of deamidation in modulating glycan-mediated cell attachment in GII.4 strains. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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17 pages, 2573 KiB  
Article
Proteomics Profiling of the Urine of Patients with Hyperthyroidism after Anti-Thyroid Treatment
by Hicham Benabdelkamel, Afshan Masood, Aishah A. Ekhzaimy and Assim A. Alfadda
Molecules 2021, 26(7), 1991; https://doi.org/10.3390/molecules26071991 - 01 Apr 2021
Cited by 5 | Viewed by 2249
Abstract
Hyperthyroidism, which is characterized by increased circulating thyroid hormone levels, alters the body’s metabolic and systemic hemodynamic balance and directly influences renal function. In this study, the urinary proteome of patients with hyperthyroidism was characterized using an untargeted proteomic approach with network analysis. [...] Read more.
Hyperthyroidism, which is characterized by increased circulating thyroid hormone levels, alters the body’s metabolic and systemic hemodynamic balance and directly influences renal function. In this study, the urinary proteome of patients with hyperthyroidism was characterized using an untargeted proteomic approach with network analysis. Urine samples were collected from nine age-matched patients before and after carbimazole treatment. Differences in the abundance of urinary proteins between hyperthyroid and euthyroid states were determined using a 2D-DIGE coupled to MALDI-TOF mass spectrometry. Alterations in the abundance of urinary proteins, analyzed via Progenesis software, revealed a statistically significant difference in abundance in a total of 40 spots corresponding to 32 proteins, 25 up and 7 down (≥1.5-fold change, ANOVA, p ≤ 0.05). The proteins identified in the study are known to regulate processes associated with cellular metabolism, transport, and acute phase response. The notable upregulated urinary proteins were serotransferrin, transthyretin, serum albumin, ceruloplasmin, alpha-1B-glycoprotein, syntenin-1, and glutaminyl peptide cyclotransferase, whereas the three notable downregulated proteins were plasma kallikrein, protein glutamine gamma-glutamyl transferase, and serpin B3 (SERPINB3). Bioinformatic analysis using ingenuity pathway analysis (IPA) identified the dysregulation of pathways associated with cellular compromise, inflammatory response, cellular assembly, and organization and identified the involvement of the APP and AKT signaling pathways via their interactions with interleukins as the central nodes. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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8 pages, 597 KiB  
Article
Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres
by Diana Canetti, Francesca Brambilla, Nigel B. Rendell, Paola Nocerino, Janet A. Gilbertson, Dario Di Silvestre, Andrea Bergamaschi, Francesca Lavatelli, Giampaolo Merlini, Julian D. Gillmore, Vittorio Bellotti, Pierluigi Mauri and Graham W. Taylor
Molecules 2021, 26(7), 1913; https://doi.org/10.3390/molecules26071913 - 29 Mar 2021
Cited by 5 | Viewed by 1783
Abstract
Amyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients’ biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial [...] Read more.
Amyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients’ biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial for clinical diagnosis and for identifying the amyloid type. Currently, the proteomic approach is routinely used at National Amyloidosis Centre (NAC, London, UK) and Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR, Milan, Italy). Both centres are members of the European Proteomics Amyloid Network (EPAN), which was established with the aim of sharing and discussing best practice in the application of amyloid proteomics. One of the EPAN’s activities was to evaluate the quality and the confidence of the results achieved using different software and algorithms for protein identification. In this paper, we report the comparison of proteomics results obtained by sharing NAC proteomics data with the ITB-CNR centre. Mass spectrometric raw data were analysed using different software platforms including Mascot, Scaffold, Proteome Discoverer, Sequest and bespoke algorithms developed for an accurate and immediate amyloid protein identification. Our study showed a high concordance of the obtained results, suggesting a good accuracy of the different bioinformatics tools used in the respective centres. In conclusion, inter-centre data exchange is a worthwhile approach for testing and validating the performance of software platforms and the accuracy of results, and is particularly important where the proteomics data contribute to a clinical diagnosis. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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17 pages, 20487 KiB  
Article
The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4
by Marek Šebela, Martin Raus, Vladan Ondřej and Petr Hašler
Molecules 2021, 26(6), 1683; https://doi.org/10.3390/molecules26061683 - 17 Mar 2021
Viewed by 1784
Abstract
The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of [...] Read more.
The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of this method is important for its use in biology and applied science. The compounds included inhibitors of respiration, glycolysis, citrate cycle, and proteosynthesis. They were used at 1–10 μM concentrations and different periods of up to 3 weeks. Cells were also grown without inhibitors in a microgravity because of expected strong effects. Mass spectra were evaluated using controls and interpreted in terms of differential peaks and their assignment to protein sequences by mass. Antibiotics, azide, and bromopyruvate had the greatest impact. The spectral patterns were markedly altered after a prolonged incubation at higher concentrations, which precluded identification in the database of reference spectra. The incubation in microgravity showed a similar effect. These differences were evident in dendrograms constructed from the spectral data. Enzyme inhibitors affected the spectra to a smaller extent. This study shows that only a long-term presence of antibiotics and strong metabolic inhibitors in the medium at 10−5 M concentrations hinders the correct identification of cyanobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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14 pages, 3440 KiB  
Article
LC-MS Quantification of Site-Specific Phosphorylation Degree by Stable-Isotope Dimethyl Labeling Coupled with Phosphatase Dephosphorylation
by Sin-Hong Chen, Ya-Chi Lin, Ming-Kuei Shih, Li-Fei Wang, Shyh-Shyan Liu and Jue-Liang Hsu
Molecules 2020, 25(22), 5316; https://doi.org/10.3390/molecules25225316 - 14 Nov 2020
Viewed by 2476
Abstract
Protein phosphorylation is a crucial post-translational modification that plays an important role in the regulation of cellular signaling processes. Site-specific quantitation of phosphorylation levels can help decipher the physiological functions of phosphorylation modifications under diverse physiological statuses. However, quantitative analysis of protein phosphorylation [...] Read more.
Protein phosphorylation is a crucial post-translational modification that plays an important role in the regulation of cellular signaling processes. Site-specific quantitation of phosphorylation levels can help decipher the physiological functions of phosphorylation modifications under diverse physiological statuses. However, quantitative analysis of protein phosphorylation degrees is still a challenging task due to its dynamic nature and the lack of an internal standard simultaneously available for the samples differently prepared for various phosphorylation extents. In this study, stable-isotope dimethyl labeling coupled with phosphatase dephosphorylation (DM + deP) was tried to determine the site-specific degrees of phosphorylation in proteins. Firstly, quantitation accuracy of the (DM + deP) approach was confirmed using synthetic peptides of various simulated phosphorylation degrees. Afterwards, it was applied to evaluate the phosphorylation stoichiometry of milk caseins. The phosphorylation degree of Ser130 on α-S1-casein was also validated by absolute quantification with the corresponding synthetic phosphorylated and nonphosphorylated peptides under a selected reaction monitoring (SRM) mode. Moreover, this (DM + deP) method was used to detect the phosphorylation degree change of Ser82 on the Hsp27 protein of HepG2 cells caused by tert-butyl hydroperoxide (t-BHP) treatment. The results showed that the absolute phosphorylation degree obtained from the (DM + deP) approach was comparable with the relative quantitation resulting from stable-isotope dimethyl labeling coupled with TiO2 enrichment. This study suggested that the (DM + deP) approach is promising for absolute quantification of site-specific degrees of phosphorylation in proteins, and it may provide more convincing information than the relative quantification method. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
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18 pages, 5348 KiB  
Article
Comparative Proteomic Analysis of Dipsacus asperoides Roots from Different Habitats in China
by Haijun Jin, Hua Yu, Haixia Wang and Jia Zhang
Molecules 2020, 25(16), 3605; https://doi.org/10.3390/molecules25163605 - 08 Aug 2020
Cited by 4 | Viewed by 2295
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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15 pages, 2056 KiB  
Article
Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis
by Masakazu Toyoshima, Yuma Tokumaru, Fumio Matsuda and Hiroshi Shimizu
Molecules 2020, 25(16), 3582; https://doi.org/10.3390/molecules25163582 - 06 Aug 2020
Cited by 13 | Viewed by 3620
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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18 pages, 2217 KiB  
Article
Plasma-Based Proteomics Profiling of Patients with Hyperthyroidism after Antithyroid Treatment
by Afshan Masood, Hicham Benabdelkamel, Aishah A. Ekhzaimy and Assim A. Alfadda
Molecules 2020, 25(12), 2831; https://doi.org/10.3390/molecules25122831 - 19 Jun 2020
Cited by 19 | Viewed by 3285
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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17 pages, 329 KiB  
Review
Unraveling the Roles of Vascular Proteins Using Proteomics
by Yan Liu, Tianbao Lin, Maria Valderrama Valencia, Cankui Zhang and Zhiqiang Lv
Molecules 2021, 26(3), 667; https://doi.org/10.3390/molecules26030667 - 27 Jan 2021
Cited by 5 | Viewed by 2300
Abstract
Vascular bundles play important roles in transporting nutrients, growth signals, amino acids, and proteins between aerial and underground tissues. In order to understand these sophisticated processes, a comprehensive analysis of the roles of the components located in the vascular tissues is required. A [...] Read more.
Vascular bundles play important roles in transporting nutrients, growth signals, amino acids, and proteins between aerial and underground tissues. In order to understand these sophisticated processes, a comprehensive analysis of the roles of the components located in the vascular tissues is required. A great deal of data has been obtained from proteomic analyses of vascular tissues in plants, which mainly aim to identify the proteins moving through the vascular tissues. Here, different aspects of the phloem and xylem proteins are reviewed, including their collection methods, and their main biological roles in growth, and biotic and abiotic stress responses. The study of vascular proteomics shows great potential to contribute to our understanding of the biological mechanisms related to development and defense in plants. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics II)
13 pages, 766 KiB  
Review
Current Status of Matrix-Assisted Laser Desorption/Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in Clinical Diagnostic Microbiology
by Sachio Tsuchida, Hiroshi Umemura and Tomohiro Nakayama
Molecules 2020, 25(20), 4775; https://doi.org/10.3390/molecules25204775 - 17 Oct 2020
Cited by 96 | Viewed by 8683
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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14 pages, 2129 KiB  
Review
Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction
by Danuta Witkowska
Molecules 2020, 25(18), 4133; https://doi.org/10.3390/molecules25184133 - 10 Sep 2020
Cited by 7 | Viewed by 2838
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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