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Special Issue "Advances and Future Perspective of Mass Spectrometry Analysis in Proteomics"

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

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 2574

Special Issue Editors

Prof. Dr. Fulvio Magni
E-Mail Website
Guest Editor
Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Vedano al Lambro, Italy
Interests: LC-MS; MALDI-imaging; biomarker discovery; phospho- and N-glycoproteome; cancer; glomerulonephrity
Dr. Marco Gaspari
E-Mail Website
Guest Editor
Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy
Interests: LC-MS; glycopeptide enrichment; biofluid proteomics; cancer proteomics; affinity purification-mass spectrometry (AP-MS)
Dr. Isabella Piga
E-Mail Website
Guest Editor
Department of Medicine and Surgery, Università degli Studi Milano-Bicocca, 20900 Vedano al Lambro, Italy
Interests: LC-MS; MALDI-imaging; biomarker discovery; method development; thyroid cancer

Special Issue Information

Dear Colleagues,

Over the last decade mass spectrometry technology has become an essential tool for proteomics research, and has been applied to a very wide range of areas such as protein profiling, protein identification and quantification, protein–protein interaction study, and post-translational modification characterization. Bottom-up (analysis of proteolytic peptide mixtures) and top-down (analysis of intact proteins) mass-spectrometry-based proteomics are the workhorse approaches to identify and characterize protein isoforms and post-translational modifications using a wide variety of sample types (i.e., cells, tissues, biofluids, food samples). A great deal of attention is paid to spatial proteomics, using mass spectrometry imaging approaches, which has paved the way for mapping the spatial localization of proteins maintaining tissue integrity, revolutionizing biomarker discovery. The phenomenal impact of mass-spectrometry-based proteomics on every field of research (from clinical study to forensic research, from environmental analysis to food analysis) is reflected in a continuous demand for novel sample preparation strategies and innovative workflow of analysis, and of statistical approaches able to process and interpret such big complex data sets.

In this context, it is a great pleasure to invite you to contribute to this Special Issue of Molecules, which will cover the latest research trends and applications in the field of mass spectrometry and proteomics, with full papers and communications describing original work as well as review articles. For review articles, a brief summary is required as a preliminary step to avoid overlapping topics.

Prof. Dr. Fulvio Magni
Dr. Marco Gaspari
Dr. Isabella Piga
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 2300 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

  • Mass spectrometry
  • sample preparation
  • protein profiling
  • biomarker discovery
  • food proteomics
  • forensic proteomics
  • clinical proteomics
  • glycoproteomics
  • method optimization
  • method development
  • post-translational modifications
  • single cell proteomics
  • mass spectrometry imaging

Published Papers (3 papers)

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Research

Article
Forensic Discrimination of Differentially Sourced Animal Blood Using a Bottom-Up Proteomics Based MALDI MS Approach
Molecules 2022, 27(7), 2039; https://doi.org/10.3390/molecules27072039 - 22 Mar 2022
Viewed by 508
Abstract
Recently published work has reported the development and application of a bottom-up proteomic approach to distinguish between human and animal blood (down to animal species level), by rapid screening using Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS). In that study, it [...] Read more.
Recently published work has reported the development and application of a bottom-up proteomic approach to distinguish between human and animal blood (down to animal species level), by rapid screening using Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS). In that study, it was additionally observed that intravenous animal blood exhibits different spectral profiles from blood collected within the animal chest cavity as well as from the diluted blood collected within packets of meat. In this follow-up study we explored the resulting hypothesis that, depending on how blood is shed or collected, protein biomarker profiles vary to the extent of systematically permitting a distinction between possible sources of blood (for example, flesh wound versus packaged meat). This intelligence may be important in reconstructing the dynamics of the crime. The combination of statistical analysis and tandem mass spectrometry has yielded additional animal blood markers as well as confirming the ability to correctly determine the animal species from which blood derived, regardless of the retailer selling it (amongst the five investigated). These data confirm the initial hypothesis and demonstrate the opportunity for the proteomics-MALDI combined approach to provide additional intelligence to the investigation of violent crimes when examining blood evidence. Full article
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Article
Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics
Molecules 2022, 27(3), 997; https://doi.org/10.3390/molecules27030997 - 01 Feb 2022
Viewed by 476
Abstract
Accurate and precise measurement of the relative protein content of blood-based samples using mass spectrometry is challenging due to the large number of circulating proteins and the dynamic range of their abundances. Traditional spectral processing methods often struggle with accurately detecting overlapping peaks [...] Read more.
Accurate and precise measurement of the relative protein content of blood-based samples using mass spectrometry is challenging due to the large number of circulating proteins and the dynamic range of their abundances. Traditional spectral processing methods often struggle with accurately detecting overlapping peaks that are observed in these samples. In this work, we develop a novel spectral processing algorithm that effectively detects over 1650 peaks with over 3.5 orders of magnitude in intensity in the 3 to 30 kD m/z range. The algorithm utilizes a convolution of the peak shape to enhance peak detection, and accurate peak fitting to provide highly reproducible relative abundance estimates for both isolated peaks and overlapping peaks. We demonstrate a substantial increase in the reproducibility of the measurements of relative protein abundance when comparing this processing method to a traditional processing method for sample sets run on multiple matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) instruments. By utilizing protein set enrichment analysis, we find a sizable increase in the number of features associated with biological processes compared to previously reported results. The new processing method could be very beneficial when developing high-performance molecular diagnostic tests in disease indications. Full article
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Article
Proteomic and Bioinformatic Analysis of Decellularized Pancreatic Extracellular Matrices
Molecules 2021, 26(21), 6740; https://doi.org/10.3390/molecules26216740 - 08 Nov 2021
Cited by 1 | Viewed by 876
Abstract
Tissue microenvironments are rich in signaling molecules. However, factors in the tissue matrix that can serve as tissue-specific cues for engineering pancreatic tissues have not been thoroughly identified. In this study, we performed a comprehensive proteomic analysis of porcine decellularized pancreatic extracellular matrix [...] Read more.
Tissue microenvironments are rich in signaling molecules. However, factors in the tissue matrix that can serve as tissue-specific cues for engineering pancreatic tissues have not been thoroughly identified. In this study, we performed a comprehensive proteomic analysis of porcine decellularized pancreatic extracellular matrix (dpECM). By profiling dpECM collected from subjects of different ages and genders, we showed that the detergent-free decellularization method developed in this study permits the preservation of approximately 62.4% more proteins than a detergent-based method. In addition, we demonstrated that dpECM prepared from young pigs contained approximately 68.5% more extracellular matrix proteins than those prepared from adult pigs. Furthermore, we categorized dpECM proteins by biological process, molecular function, and cellular component through gene ontology analysis. Our study results also suggested that the protein composition of dpECM is significantly different between male and female animals while a KEGG enrichment pathway analysis revealed that dpECM protein profiling varies significantly depending on age. This study provides the proteome of pancreatic decellularized ECM in different animal ages and genders, which will help identify the bioactive molecules that are pivotal in creating tissue-specific cues for engineering tissues in vitro. Full article
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