Special Issue "Proteomics: Technologies and Their Applications"

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: 30 September 2020.

Special Issue Editors

Dr. Delphine Vincent
Website
Guest Editor
Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
Interests: proteomics; secretomics; bottom–up; middle–down; top–down; gel-free; liquid chromatography; tandem mass spectrometry; data mining; statistical analysis
Dr. Simone Rochfort
Website
Guest Editor
Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
Interests: proteomics; metabolomics; quantitation; chromatography; mass spectrometry; nuclear magnetic resonance
Dr. David Quilici
Website
Guest Editor
University of Nevada, Reno, Reno, United States
Interests: proteomics; mass spectrometry; quantitative proteomics; bottom–up; liquid chromatography
Dr. Ludovic Bonhomme
Website
Guest Editor
INRA, UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
Interests: dual proteomics; secretomics; phosphoproteomics; data mining; data integration; multivariate statistics

Special Issue Information

Dear Colleagues,

Proteins are complex molecules that catalyze reactions, transmit signals, and create cellular support structures organized in a spatial and temporal manner. A set of proteins is referred to as a proteome when considered globally in a system of interest whether it be organelle, cell, tissue, organ, or species. The proteome is made of all the proteoforms arising from gene mutations and polymorphisms, RNA processing, and posttranslational modifications (PTMs) such as acetylation, methylation, phosphorylation, glycosylation, and protein degradation, which are not encoded in the genome. The ability to characterize these proteoforms is essential for a thorough understanding of the biological mechanisms involved in the studied system. Proteomics, the science of analyzing proteomes, always involves protein recovery, separation, and mass spectrometry (MS) for quantitation and identification purposes. Consequently, progress in proteomics is tightly linked with technical advances in sample preparation, chromatography, electrophoresis, and MS. A key aspect of proteomics success relies on the correct identification of all the proteoforms observed in a sample in a high throughput manner. This topic covers innovations and technical progresses in these areas and welcomes original research, technical notes, methods papers, and reviews.

Dr. Delphine Vincent
Dr. Simone Rochfort
Dr. David Quilici
Dr. Ludovic Bonhomme
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.ynsqex.icu 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. Proteomes is an international peer-reviewed open access quarterly 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 1000 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

  • separation techniques
  • liquid chromatography
  • capillary electrophorosis
  • gel electrophoresis
  • mass spectrometry
  • LC–MS
  • tandem mass spectrometry
  • LC-MS/MS
  • shotgun proteomics
  • native mass spectrometry
  • high accuracy
  • quantitation
  • proteoforms
  • post-translational modifications
  • glycosylation
  • proteins
  • peptides
  • biomarkers

Published Papers (1 paper)

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Research

Open AccessFeature PaperArticle
The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines
Proteomes 2020, 8(2), 13; https://doi.org/10.3390/proteomes8020013 - 15 Jun 2020
Abstract
Cannabis research has taken off since the relaxation of legislation, yet proteomics is still lagging. In 2019, we published three proteomics methods aimed at optimizing protein extraction, protein digestion for bottom-up and middle-down proteomics, as well as the analysis of intact proteins for [...] Read more.
Cannabis research has taken off since the relaxation of legislation, yet proteomics is still lagging. In 2019, we published three proteomics methods aimed at optimizing protein extraction, protein digestion for bottom-up and middle-down proteomics, as well as the analysis of intact proteins for top-down proteomics. The database of Cannabis sativa proteins used in these studies was retrieved from UniProt, the reference repositories for proteins, which is incomplete and therefore underrepresents the genetic diversity of this non-model species. In this fourth study, we remedy this shortcoming by searching larger databases from various sources. We also compare two search engines, the oldest, SEQUEST, and the most popular, Mascot. This shotgun proteomics experiment also utilizes the power of parallel digestions with orthogonal proteases of increasing selectivity, namely chymotrypsin, trypsin/Lys-C and Asp-N. Our results show that the larger the database the greater the list of accessions identified but the longer the duration of the search. Using orthogonal proteases and different search algorithms increases the total number of proteins identified, most of them common despite differing proteases and algorithms, but many of them unique as well. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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