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Special Issue "Mass Spectrometric Proteomics"

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

Deadline for manuscript submissions: 30 September 2018

Special Issue Editor

Guest Editor
Prof. Dr. Paolo Iadarola

Department of Biology and Biotechnologies “L. Spallanzani”, Biochemistry Unit, University of Pavia, Italy
Website | E-Mail
Interests: methods in biochemistry; investigation of the proteome of different tissues/fluids by using the classical methods of proteomics; purification and characterization of enzymes and structural proteins; electrophoresis;2‐DE;liquid chromatography;LC-MS;proteomics;human fluids;metabolomics

Special Issue Information

Dear Colleagues,

A comprehensive understanding of the biochemical processes that govern life requires a deep understanding of the information encoded in the genome, and that relate to all protein forms expressed in a biological system, i.e., the proteome. While being complementary to each other, only proteome, that differs from cell to cell and changes, even for a single cell, in response to different stimuli, is descriptive of a biological phenotype. Detecting and quantifying all proteins, studying their post-translational modifications, level of expression, localization, interaction, and domain structure are the goals of proteomics. Because of its ability to handle the complexity of the events mentioned above, mass spectrometry (MS) has become an indispensable tool for proteomics. However, what does the term MS stand for? MS consists of a variety of analytical methods, each characterized by its own strengths for the solution of a peculiar problem and of which the choice depends on the aim of the study. The numerous developed applications of MS in proteomics, thus far, have contributed heavily to new insights into the roles played by some proteins in human disorders.

The aim of this Special Issue is to attract contributions on all aspects of MS-based proteomics with a special emphasis on recent/novel technologies that, by pushing the boundary of MS capabilities, make them able to address biological problems that have not yet been faced.

Prof. Dr. Paolo Iadarola
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 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 monthly 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 1800 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

  • proteome
  • mass spectrometry
  • biological system
  • genome
  • protein forms
  • biological phenotype
  • expression, localization, interaction and domain structure of proteomics

Published Papers (3 papers)

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Research

Open AccessArticle Comparative Proteomic Analysis of Rana chensinensis Oviduct
Molecules 2018, 23(6), 1384; https://doi.org/10.3390/molecules23061384
Received: 8 March 2018 / Revised: 31 May 2018 / Accepted: 5 June 2018 / Published: 8 June 2018
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Abstract
As one of most important traditional Chinese medicine resources, the oviduct of female Rana chensinensis (Chinese brown frog) was widely used in the treatment of asthenia after sickness or delivery, deficiency in vigor, palpitation, and insomnia. Unlike other vertebrates, the oviduct of Rana
[...] Read more.
As one of most important traditional Chinese medicine resources, the oviduct of female Rana chensinensis (Chinese brown frog) was widely used in the treatment of asthenia after sickness or delivery, deficiency in vigor, palpitation, and insomnia. Unlike other vertebrates, the oviduct of Rana chensinensis oviduct significantly expands during prehibernation, in contrast to the breeding period. To explain this phenomenon at the molecular level, the protein expression profiles of Rana chensinensis oviduct during the breeding period and prehibernation were observed using isobaric tags for relative and absolute quantitation (iTRAQ) technique. Then, all identified proteins were used to obtain gene ontology (GO) annotation. Ultimately, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis was performed to predict the pathway on differentially expressed proteins (DEPs). A total of 4479 proteins were identified, and 312 of them presented different expression profiling between prehibernation and breeding period. Compared with prehibernation group, 86 proteins were upregulated, and 226 proteins were downregulated in breeding period. After KEGG enrichment analysis, 163 DEPs were involved in 6 pathways, which were lysosome, RNA transport, glycosaminoglycan degradation, extracellular matrix (ECM)–receptor interaction, metabolic pathways and focal adhesion. This is the first report on the protein profiling of Rana chensinensis oviduct during the breeding period and prehibernation. Results show that this distinctive physiological phenomenon of Rana chensinensis oviduct was mainly involved in ECM–receptor interaction, metabolic pathways, and focal adhesion. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics)
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Figure 1a

Open AccessArticle Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE Mutant Strains of Synechocystis sp. PCC 6803
Molecules 2018, 23(5), 1051; https://doi.org/10.3390/molecules23051051
Received: 9 April 2018 / Revised: 27 April 2018 / Accepted: 27 April 2018 / Published: 1 May 2018
PDF Full-text (2793 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A targeted proteome analysis was conducted to investigate the SigE dependent-regulation of central metabolism in Synechocystis sp. PCC 6803 by directly comparing the protein abundance profiles among the wild type, a sigE deletion mutant (ΔsigE), and a sigE over-expression (sigE
[...] Read more.
A targeted proteome analysis was conducted to investigate the SigE dependent-regulation of central metabolism in Synechocystis sp. PCC 6803 by directly comparing the protein abundance profiles among the wild type, a sigE deletion mutant (ΔsigE), and a sigE over-expression (sigEox) strains. Expression levels of 112 target proteins, including the central metabolism related-enzymes and the subunits of the photosystems, were determined by quantifying the tryptic peptides in the multiple reaction monitoring (MRM) mode of liquid-chromatography–triple quadrupole mass spectrometry (LC–MS/MS). Comparison with gene-expression data showed that although the abundance of Gnd protein was closely correlated with that of gnd mRNA, there were poor correlations for GdhA/gdhA and glycogen degradation-related genes such as GlgX/glgX and GlgP/glgP pairs. These results suggested that the regulation of protein translation and degradation played a role in regulating protein abundance. The protein abundance profile suggested that SigE overexpression reduced the proteins involved in photosynthesis and increased GdhA abundance, which is involved in the nitrogen assimilation pathway using NADPH. The results obtained in this study successfully demonstrated that targeted proteome analysis enables direct comparison of the abundance of central metabolism- and photosystem-related proteins. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics)
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Open AccessArticle Identification of Ophiocordyceps sinensis and Its Artificially Cultured Ophiocordyceps Mycelia by Ultra-Performance Liquid Chromatography/Orbitrap Fusion Mass Spectrometry and Chemometrics
Molecules 2018, 23(5), 1013; https://doi.org/10.3390/molecules23051013
Received: 25 March 2018 / Revised: 18 April 2018 / Accepted: 19 April 2018 / Published: 26 April 2018
PDF Full-text (5143 KB) | HTML Full-text | XML Full-text
Abstract
Since the cost of Ophiocordyceps sinensis, an important fungal drug used in Chinese medicine, has increased dramatically, and the counterfeits may have adverse health effects, a rapid and precise marker using the peptide mass spectrometry identification system could significantly enhance the regulatory
[...] Read more.
Since the cost of Ophiocordyceps sinensis, an important fungal drug used in Chinese medicine, has increased dramatically, and the counterfeits may have adverse health effects, a rapid and precise marker using the peptide mass spectrometry identification system could significantly enhance the regulatory capacity. In this study, we determined the marker peptides in the digested mixtures of fungal proteins in wild O. sinensis fruiting bodies and various commercially available mycelium fermented powders using ultra-performance liquid chromatography/Orbitrap Fusion mass spectrometry coupled with chemometrics. The results indicated the following marker peptides: TLLEAIDSIEPPK (m/z 713.39) was identified in the wild O. sinensis fruiting body, AVLSDAITLVR (m/z 579.34) was detected in the fermented O. sinensis mycelium powder, FAELLEK (m/z 849.47) was found in the fermented Ophiocordyceps mycelium powder, LESVVTSFTK (m/z 555.80) was discovered in the artificial Ophiocordyceps mycelium powder, and VPSSAVLR (m/z 414.75) was observed in O. mortierella mycelium powder. In order to verify the specificity and applicability of the method, the five marker peptides were synthesized and tested on all samples. All in all, to the best of our knowledge, this is the first time that mass spectrometry has been employed to detect the marker peptides of O.sinensis and its related products. Full article
(This article belongs to the Special Issue Mass Spectrometric Proteomics)
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Figure 1a

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: A LITTLE KNOWN TRYPSIN ISOFORM
Article type: Review
Authors: Zdeněk PERUTKA and Marek ŠEBELA
Affiliation: Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic

Title: Proteomics Of Chronic Obstructive Pulmonary Disease: Could These Data Help Clinicians For A Better Understanding Of This Severe Disorder?
Article type: Review
Authors: S. Viglio 1, M. Cagnone 1, R. Salvini 1, A. Bardoni 1, M. Fumagalli 2 and P. Iadarola 2
Affiliations:
1. Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
2. Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Italy
Abstract: Chronic Obstructive Pulmonary Disease (COPD) is an “umbrella” term that combines different pathological conditions such as emphysema, chronic bronchitis, non-reversible asthma and some types of bronchiectasis characterized by irreversible airflow limitations. Cigarette smoking, while being the main cause of the disorder, is not the only one. In fact, continuous inhalation of toxic gases and particles which promote chronic airway inflammation, as well as genetic factors, i.e. the deficiency of α1-antitrypsin, may contribute to the development of this pathology. Being COPD very heterogeneous and potentially representing several disease phenotypes, an early correct diagnosis of this disorder may be difficult. It is a common opinion that the finding of specific molecular markers of a disease would strongly contribute to speeding up its diagnosis thus developing a possible treatment and/or making it more effective. With the advent of proteomics, identification of proteins in different organs/tissues, aimed at understanding whether they represent a helpful tool for monitoring alterations in these districts, has become an area of increasing interest. Aim of this review article is to keep the reader informed about the proteomic data produced in the last ten years in the field of pulmonary disorders with special emphasis on COPD. Taken together, the results documented here demonstrate that, after a few years of activity, proteomics of COPD is catching up with its promise. The constantly growing number of reports in this area supports the view of this approach as one of the decisive methodological tools for the identification/characterization of disease-associated proteins.

 

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