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Advanced Applications of Mass Spectrometry for Proteomics Analysis
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Advanced Applications of Mass Spectrometry for Proteomics Analysis

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

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 9800

Special Issue Editor

Dr. Richard Wilson

E-Mail Website
Guest Editor
Central Science Laboratory, University of Tasmania, Hobart, Tasmania 7001, Australia
Interests: proteomics; mass spectrometry; bioinformatics; sample preparation; extracellular matrix

Special Issue Information

Dear Colleagues,

Mass spectrometry is firmly established as an essential analytical technique in almost every branch of the life sciences, and in particular biomedical research. It is at the heart of proteomics, the term given to large-scale and/or unbiased protein identification, quantitation, and characterization. Advances in proteomics-based research are underpinned by new technologies and methods, and this Special Edition aims to highlight recent developments including but not limited to sample preparation, applications of data-independent acquisition, micro-scale analysis, and characterization of post-translational modifications.

Dr. Richard Wilson
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 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
  • sample preparation
  • DIA
  • post-translational modifications
  • biomarker discovery
  • ion mobility

Published Papers (5 papers)

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Research

17 pages, 5518 KiB  
Article
Optimized Sample Preparation and Microscale Separation Methods for High-Sensitivity Analysis of Hydrophilic Peptides
by Gábor Tóth, Simon Sugár, Mirjam Balbisi, Balázs András Molnár, Fanni Bugyi, Kata Dorina Fügedi, László Drahos and Lilla Turiák
Molecules 2022, 27(19), 6645; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27196645 - 06 Oct 2022
Cited by 4 | Viewed by 1922
Abstract
The optimization of solid-phase extraction (SPE) purification and chromatographic separation is usually neglected during proteomics studies. However, the effects on detection performance are not negligible, especially when working with highly glycosylated samples. We performed a comparative study of different SPE setups, including an [...] Read more.
The optimization of solid-phase extraction (SPE) purification and chromatographic separation is usually neglected during proteomics studies. However, the effects on detection performance are not negligible, especially when working with highly glycosylated samples. We performed a comparative study of different SPE setups, including an in-house optimized method and reversed-phase chromatographic gradients for the analysis of highly glycosylated plasma fractions as a model sample for glycopeptide analysis. The in-house-developed SPE method outperformed the graphite-based and hydrophilic interaction liquid chromatography (HILIC) purification methods in detection performance, recovery, and repeatability. During optimization of the chromatography, peak distribution was maximized to increase the peptide detection rate. As a result, we present sample purification and chromatographic separation methods optimized for the analysis of hydrophilic samples, the most important of which is heavily N-glycosylated protein mixtures. Full article
(This article belongs to the Special Issue Advanced Applications of Mass Spectrometry for Proteomics Analysis)
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15 pages, 2208 KiB  
Article
Comparative Proteomic Analysis of Potato Roots from Resistant and Susceptible Cultivars to Spongospora subterranea Zoospore Root Attachment In Vitro
by Xian Yu, Richard Wilson, Sadegh Balotf, Robert S. Tegg, Alieta Eyles and Calum R. Wilson
Molecules 2022, 27(18), 6024; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27186024 - 15 Sep 2022
Cited by 2 | Viewed by 1482
Abstract
Potato (Solanum tuberosum L.) exhibits broad variations in cultivar resistance to tuber and root infections by the soilborne, obligate biotrophic pathogen Spongospora subterranea. Host resistance has been recognised as an important approach in potato disease management, whereas zoospore root attachment has [...] Read more.
Potato (Solanum tuberosum L.) exhibits broad variations in cultivar resistance to tuber and root infections by the soilborne, obligate biotrophic pathogen Spongospora subterranea. Host resistance has been recognised as an important approach in potato disease management, whereas zoospore root attachment has been identified as an effective indicator for the host resistance to Spongospora root infection. However, the mechanism of host resistance to zoospore root attachment is currently not well understood. To identify the potential basis for host resistance to S. subterranea at the molecular level, twelve potato cultivars differing in host resistance to zoospore root attachment were used for comparative proteomic analysis. In total, 3723 proteins were quantified from root samples across the twelve cultivars using a data-independent acquisition mass spectrometry approach. Statistical analysis identified 454 proteins that were significantly more abundant in the resistant cultivars; 626 proteins were more abundant in the susceptible cultivars. In resistant cultivars, functional annotation of the proteomic data indicated that Gene Ontology terms related to the oxidative stress and metabolic processes were significantly over-represented. KEGG pathway analysis identified that the phenylpropanoid biosynthesis pathway was associated with the resistant cultivars, suggesting the potential role of lignin biosynthesis in the host resistance to S. subterranea. Several enzymes involved in pectin biosynthesis and remodelling, such as pectinesterase and pectin acetylesterase, were more abundant in the resistant cultivars. Further investigation of the potential role of root cell wall pectin revealed that the pectinase treatment of roots resulted in a significant reduction in zoospore root attachment in both resistant and susceptible cultivars. This study provides a comprehensive proteome-level overview of resistance to S. subterranea zoospore root attachment across twelve potato cultivars and has identified a potential role for cell wall pectin in regulating zoospore root attachment. Full article
(This article belongs to the Special Issue Advanced Applications of Mass Spectrometry for Proteomics Analysis)
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15 pages, 2097 KiB  
Article
Translational Proteomic Approach for Cholangiocarcinoma Biomarker Discovery, Validation, and Multiplex Assay Development: A Pilot Study
by Kamolwan Watcharatanyatip, Somchai Chutipongtanate, Daranee Chokchaichamnankit, Churat Weeraphan, Kanokwan Mingkwan, Virat Luevisadpibul, David S. Newburg, Ardythe L. Morrow, Jisnuson Svasti and Chantragan Srisomsap
Molecules 2022, 27(18), 5904; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27185904 - 11 Sep 2022
Cited by 2 | Viewed by 1648
Abstract
Cholangiocarcinoma (CCA) is a highly lethal disease because most patients are asymptomatic until they progress to advanced stages. Current CCA diagnosis relies on clinical imaging tests and tissue biopsy, while specific CCA biomarkers are still lacking. This study employed a translational proteomic approach [...] Read more.
Cholangiocarcinoma (CCA) is a highly lethal disease because most patients are asymptomatic until they progress to advanced stages. Current CCA diagnosis relies on clinical imaging tests and tissue biopsy, while specific CCA biomarkers are still lacking. This study employed a translational proteomic approach for the discovery, validation, and development of a multiplex CCA biomarker assay. In the discovery phase, label-free proteomic quantitation was performed on nine pooled plasma specimens derived from nine CCA patients, nine disease controls (DC), and nine normal individuals. Seven proteins (S100A9, AACT, AFM, and TAOK3 from proteomic analysis, and NGAL, PSMA3, and AMBP from previous literature) were selected as the biomarker candidates. In the validation phase, enzyme-linked immunosorbent assays (ELISAs) were applied to measure the plasma levels of the seven candidate proteins from 63 participants: 26 CCA patients, 17 DC, and 20 normal individuals. Four proteins, S100A9, AACT, NGAL, and PSMA3, were significantly increased in the CCA group. To generate the multiplex biomarker assays, nine machine learning models were trained on the plasma dynamics of all seven candidates (All-7 panel) or the four significant markers (Sig-4 panel) from 45 of the 63 participants (70%). The best-performing models were tested on the unseen values from the remaining 18 (30%) of the 63 participants. Very strong predictive performances for CCA diagnosis were obtained from the All-7 panel using a support vector machine with linear classification (AUC = 0.96; 95% CI 0.88–1.00) and the Sig-4 panel using partial least square analysis (AUC = 0.94; 95% CI 0.82–1.00). This study supports the use of the composite plasma biomarkers measured by clinically compatible ELISAs coupled with machine learning models to identify individuals at risk of CCA. The All-7 and Sig-4 assays for CCA diagnosis should be further validated in an independent prospective blinded clinical study. Full article
(This article belongs to the Special Issue Advanced Applications of Mass Spectrometry for Proteomics Analysis)
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12 pages, 2190 KiB  
Article
Investigation of the N-Glycosylation of the SARS-CoV-2 S Protein Contained in VLPs Produced in Nicotiana benthamiana
by Juliette Balieu, Jae-Wan Jung, Philippe Chan, George P. Lomonossoff, Patrice Lerouge and Muriel Bardor
Molecules 2022, 27(16), 5119; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27165119 - 11 Aug 2022
Cited by 7 | Viewed by 2183
Abstract
The emergence of the SARS-CoV-2 coronavirus pandemic in China in late 2019 led to the fast development of efficient therapeutics. Of the major structural proteins encoded by the SARS-CoV-2 genome, the SPIKE (S) protein has attracted considerable research interest because of the central [...] Read more.
The emergence of the SARS-CoV-2 coronavirus pandemic in China in late 2019 led to the fast development of efficient therapeutics. Of the major structural proteins encoded by the SARS-CoV-2 genome, the SPIKE (S) protein has attracted considerable research interest because of the central role it plays in virus entry into host cells. Therefore, to date, most immunization strategies aim at inducing neutralizing antibodies against the surface viral S protein. The SARS-CoV-2 S protein is heavily glycosylated with 22 predicted N-glycosylation consensus sites as well as numerous mucin-type O-glycosylation sites. As a consequence, O- and N-glycosylations of this viral protein have received particular attention. Glycans N-linked to the S protein are mainly exposed at the surface and form a shield-masking specific epitope to escape the virus antigenic recognition. In this work, the N-glycosylation status of the S protein within virus-like particles (VLPs) produced in Nicotiana benthamiana (N. benthamiana) was investigated using a glycoproteomic approach. We show that 20 among the 22 predicted N-glycosylation sites are dominated by complex plant N-glycans and one carries oligomannoses. This suggests that the SARS-CoV-2 S protein produced in N. benthamiana adopts an overall 3D structure similar to that of recombinant homologues produced in mammalian cells. Full article
(This article belongs to the Special Issue Advanced Applications of Mass Spectrometry for Proteomics Analysis)
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10 pages, 1597 KiB  
Communication
Aqueous Solutions of Peptides and Trialkylamines Lead to Unexpected Peptide Modification
by Yiran Ma, Puja J. Gandhi and James P. Reilly
Molecules 2021, 26(21), 6481; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26216481 - 27 Oct 2021
Viewed by 1835
Abstract
When trialkylamines are added to buffered solutions of peptides, unexpected adducts can be formed. These adducts correspond to Schiff base products. The source of the reaction is the unexpected presence of aldehydes in amines. The aldehydes can be detected in a few ways. [...] Read more.
When trialkylamines are added to buffered solutions of peptides, unexpected adducts can be formed. These adducts correspond to Schiff base products. The source of the reaction is the unexpected presence of aldehydes in amines. The aldehydes can be detected in a few ways. Most importantly, they can lead to unanticipated results in proteomics experiments. Their undesirable effects can be minimized through the addition of other amines. Full article
(This article belongs to the Special Issue Advanced Applications of Mass Spectrometry for Proteomics Analysis)
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