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Proteomes
Special Issues
Proteomics: Technologies and Their Applications
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Proteomics: Technologies and Their Applications

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

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 21636

Special Issue Editors

Dr. Delphine Vincent

E-Mail Website
Guest Editor
Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
Interests: proteomics; secretomics; bottom–up; middle–down; top–down; gel-free; liquid chromatography; tandem mass spectrometry; data mining; statistical analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Simone Rochfort

E-Mail Website
Guest Editor
Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
Interests: proteomics; metabolomics; quantitation; chromatography; mass spectrometry; nuclear magnetic resonance
Dr. David Quilici

E-Mail Website
Guest Editor
University of Nevada, Reno, NV, USA
Interests: proteomics; mass spectrometry; quantitative proteomics; bottom–up; liquid chromatography
Dr. Ludovic Bonhomme

E-Mail 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.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. 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 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

  • 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 (6 papers)

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Research

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14 pages, 2104 KiB  
Article
The New and the Old: Platform Cross-Validation of Immunoaffinity MASS Spectrometry versus ELISA for PromarkerD, a Predictive Test for Diabetic Kidney Disease
by Scott Bringans, Kirsten Peters, Tammy Casey, Jason Ito and Richard Lipscombe
Proteomes 2020, 8(4), 31; https://0-doi-org.brum.beds.ac.uk/10.3390/proteomes8040031 - 28 Oct 2020
Cited by 6 | Viewed by 2728
Abstract
PromarkerD is a proteomics derived test for predicting diabetic kidney disease that measures the concentrations of three plasma protein biomarkers, APOA4, CD5L and IBP3. Antibodies against these proteins were developed and applied to a multiplexed immunoaffinity capture mass spectrometry assay. In parallel, and [...] Read more.
PromarkerD is a proteomics derived test for predicting diabetic kidney disease that measures the concentrations of three plasma protein biomarkers, APOA4, CD5L and IBP3. Antibodies against these proteins were developed and applied to a multiplexed immunoaffinity capture mass spectrometry assay. In parallel, and facilitating current clinical laboratory workflows, a standard ELISA was also developed to measure each protein. The performance characteristics of the two technology platforms were compared using a cohort of 100 samples, with PromarkerD test scores demonstrating a high correlation (R = 0.97). These technologies illustrate the potential for large scale, high throughput clinical applications of proteomics now and into the future. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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11 pages, 2013 KiB  
Article
PeptideWitch–A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data
by David C. L. Handler, Flora Cheng, Abdulrahman M. Shathili and Paul A. Haynes
Proteomes 2020, 8(3), 21; https://0-doi-org.brum.beds.ac.uk/10.3390/proteomes8030021 - 21 Aug 2020
Cited by 2 | Viewed by 3183
Abstract
PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics analysis using normalised spectral abundance factors. The program inputs are low stringency protein identification lists output [...] Read more.
PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics analysis using normalised spectral abundance factors. The program inputs are low stringency protein identification lists output from peptide-to-spectrum matching search engines for ‘control’ and ‘treated’ samples. Through a combination of spectral count summation and inner joins, PeptideWitch processes low stringency data, and outputs high stringency data that are suitable for downstream quantitation. Data quality metrics are generated, and a series of statistical analyses and graphical representations are presented, aimed at defining and presenting the difference between the two sample proteomes. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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25 pages, 2046 KiB  
Article
The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines
by Delphine Vincent, Keith Savin, Simone Rochfort and German Spangenberg
Proteomes 2020, 8(2), 13; https://0-doi-org.brum.beds.ac.uk/10.3390/proteomes8020013 - 15 Jun 2020
Cited by 3 | Viewed by 3716
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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Review

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20 pages, 1318 KiB  
Review
Misincorporation Proteomics Technologies: A Review
by Joel R. Steele, Carly J. Italiano, Connor R. Phillips, Jake P. Violi, Lisa Pu, Kenneth J. Rodgers and Matthew P. Padula
Proteomes 2021, 9(1), 2; https://0-doi-org.brum.beds.ac.uk/10.3390/proteomes9010002 - 21 Jan 2021
Cited by 5 | Viewed by 4179 | Correction
Abstract
Proteinopathies are diseases caused by factors that affect proteoform conformation. As such, a prevalent hypothesis is that the misincorporation of noncanonical amino acids into a proteoform results in detrimental structures. However, this hypothesis is missing proteomic evidence, specifically the detection of a noncanonical [...] Read more.
Proteinopathies are diseases caused by factors that affect proteoform conformation. As such, a prevalent hypothesis is that the misincorporation of noncanonical amino acids into a proteoform results in detrimental structures. However, this hypothesis is missing proteomic evidence, specifically the detection of a noncanonical amino acid in a peptide sequence. This review aims to outline the current state of technology that can be used to investigate mistranslations and misincorporations whilst framing the pursuit as Misincorporation Proteomics (MiP). The current availability of technologies explored herein is mass spectrometry, sample enrichment/preparation, data analysis techniques, and the hyphenation of approaches. While many of these technologies show potential, our review reveals a need for further development and refinement of approaches is still required. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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26 pages, 1010 KiB  
Review
What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?
by Katrin Marcus, Cécile Lelong and Thierry Rabilloud
Proteomes 2020, 8(3), 17; https://doi.org/10.3390/proteomes8030017 - 06 Aug 2020
Cited by 43 | Viewed by 5223
Abstract
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis [...] Read more.
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit. Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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Other

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2 pages, 159 KiB  
Correction
Correction: Steele et al. Misincorporation Proteomics Technologies: A Review. Proteomes 2021, 9, 2
by Joel R. Steele, Carly J. Italiano, Connor R. Phillips, Jake P. Violi, Lisa Pu, Kenneth J. Rodgers and Matthew P. Padula
Proteomes 2022, 10(2), 22; https://0-doi-org.brum.beds.ac.uk/10.3390/proteomes10020022 - 16 Jun 2022
Viewed by 1494
Abstract
In the original publication, there was a mistake in Table 2 as published [...] Full article
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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