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Proteomes
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Quantitative Proteomics: Techniques and Applications
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Quantitative Proteomics: Techniques and Applications

A special issue of Proteomes (ISSN 2227-7382). This special issue belongs to the section "Proteomics Technology and Methodology Development".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 16778

Special Issue Editor

Dr. Joao A. Paulo

E-Mail Website
Guest Editor
Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Interests: mass spectrometry-base proteomics; method development; quality control; sample preparation; automation; data acquisition optimization; phosphoproteomics; signaling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Quantitative proteomics is a rapidly developing field that is providing new insights into the structure, function, and regulation of proteins. This Special Issue of Proteomes will focus on the latest techniques and applications in quantitative proteomics.

The most common techniques used in quantitative proteomics include isobaric tagging, targeted proteomics, and label-free methods. Isobaric tagging methods use stable isotopes to label proteins or peptides, which allows for the simultaneous measurement of multiple samples in a single experiment. Targeted proteomics methods focus on the quantification of specific proteins or peptides, while label-free methods do not require the use of any labels.

Quantitative proteomics has a wide range of applications, including studying protein expression changes in response to different conditions, identifying protein-protein interactions, characterizing protein post-translational modifications, and determining the structure of proteins.

This Special Issue of Proteomes is soliciting original research articles, review articles, and mini-reviews on all aspects of quantitative proteomics. We encourage submissions that describe new techniques, applications, or data analysis methods.

Dr. Joao A. Paulo
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. 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

  • proteomics
  • isobaric tagging
  • targeted proteomics
  • DIA
  • label-free quantification
  • mass spectrometry

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Published Papers (6 papers)

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Research

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19 pages, 9666 KiB  
Article
Plasma and Kidney Proteome Profiling Combined with Laser Capture Microdissection Reveal Large Increases in Immunoglobulins with Age
by Leanne J. G. Chan, Niclas Olsson, Magdalena Preciado López, Kayley Hake, Haruna Tomono, Matthew A. Veras and Fiona E. McAllister
Proteomes 2024, 12(2), 16; https://doi.org/10.3390/proteomes12020016 - 3 Jun 2024
Viewed by 4152
Abstract
One of the main hallmarks of aging is aging-associated inflammation, also known as inflammaging. In this study, by comparing plasma and kidney proteome profiling of young and old mice using LC–MS profiling, we discovered that immunoglobulins are the proteins that exhibit the highest [...] Read more.
One of the main hallmarks of aging is aging-associated inflammation, also known as inflammaging. In this study, by comparing plasma and kidney proteome profiling of young and old mice using LC–MS profiling, we discovered that immunoglobulins are the proteins that exhibit the highest increase with age. This observation seems to have been disregarded because conventional proteome profiling experiments typically overlook the expression of high-abundance proteins or employ depletion methods to remove them before LC–MS analysis. We show that proteome profiling of immunoglobulins will likely be a useful biomarker of aging. Spatial profiling using immunofluorescence staining of kidney sections indicates that the main increases in immunoglobulins with age are localized in the glomeruli of the kidney. Using laser capture microdissection coupled with LC–MS, we show an increase in multiple immune-related proteins in glomeruli from aged mice. Increased deposition of immunoglobulins, immune complexes, and complement proteins in the kidney glomeruli may be a factor leading to reduced filtering capacity of the kidney with age. Therapeutic strategies to reduce the deposition of immunoglobulins in the kidney may be an attractive strategy for healthy aging. Full article
(This article belongs to the Special Issue Quantitative Proteomics: Techniques and Applications)
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19 pages, 7120 KiB  
Article
Quantitative Proteomics Reveal Region-Specific Alterations in Neuroserpin-Deficient Mouse Brain and Retina: Insights into Serpini1 Function
by Shahab Mirshahvaladi, Nitin Chitranshi, Ardeshir Amirkhani, Rashi Rajput, Devaraj Basavarajappa, Roshana Vander Wall, Dana Pascovici, Angela Godinez, Giovanna Galliciotti, Joao A. Paulo, Veer Gupta, Stuart L. Graham, Vivek Gupta and Mehdi Mirzaei
Proteomes 2024, 12(1), 7; https://doi.org/10.3390/proteomes12010007 - 14 Mar 2024
Viewed by 2782
Abstract
Neural regeneration and neuroprotection represent strategies for future management of neurodegenerative disorders such as Alzheimer’s disease (AD) or glaucoma. However, the complex molecular mechanisms that are involved in neuroprotection are not clearly understood. A promising candidate that maintains neuroprotective signaling networks is neuroserpin [...] Read more.
Neural regeneration and neuroprotection represent strategies for future management of neurodegenerative disorders such as Alzheimer’s disease (AD) or glaucoma. However, the complex molecular mechanisms that are involved in neuroprotection are not clearly understood. A promising candidate that maintains neuroprotective signaling networks is neuroserpin (Serpini1), a serine protease inhibitor expressed in neurons which selectively inhibits extracellular tissue-type plasminogen activator (tPA)/plasmin and plays a neuroprotective role during ischemic brain injury. Abnormal function of this protein has been implicated in several conditions including stroke, glaucoma, AD, and familial encephalopathy with neuroserpin inclusion bodies (FENIB). Here, we explore the potential biochemical roles of Serpini1 by comparing proteome changes between neuroserpin-deficient (NS−/−) and control mice, in the retina (RE), optic nerve (ON), frontal cortex (FC), visual cortex (VC), and cerebellum (CB). To achieve this, a multiple-plex quantitative proteomics approach using isobaric tandem mass tag (TMT) technology was employed followed by functional enrichment and protein–protein interaction analysis. We detected around 5000 proteins in each tissue and a pool of 6432 quantified proteins across all regions, resulting in a pool of 1235 differentially expressed proteins (DEPs). Principal component analysis and hierarchical clustering highlighted similarities and differences in the retina compared to various brain regions, as well as differentiating NS−/− proteome signatures from control samples. The visual cortex revealed the highest number of DEPs, followed by cerebellar regions. Pathway analysis unveiled region-specific changes, including visual perception, focal adhesion, apoptosis, glutamate receptor activation, and supramolecular fiber organization in RE, ON, FC, VC, and CB, respectively. These novel findings provide comprehensive insights into the region-specific networking of Serpini1 in the central nervous system, further characterizing its potential role as a neuroprotective agent. Data are available via ProteomeXchange with identifier PXD046873. Full article
(This article belongs to the Special Issue Quantitative Proteomics: Techniques and Applications)
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20 pages, 20372 KiB  
Article
Proteome-Wide Profiling Using Sample Multiplexing of a Human Cell Line Treated with Cannabidiol (CBD) and Tetrahydrocannabinol (THC)
by Morteza Abyadeh, Vivek Gupta, Xinyue Liu, Valentina Rossio, Mehdi Mirzaei, Jennifer Cornish, Joao A. Paulo and Paul A. Haynes
Proteomes 2023, 11(4), 36; https://doi.org/10.3390/proteomes11040036 - 2 Nov 2023
Viewed by 2697
Abstract
Cannabis has been used historically for both medicinal and recreational purposes, with the most notable cannabinoids being cannabidiol (CBD) and tetrahydrocannabinol (THC). Although their therapeutic effects have been well studied and their recreational use is highly debated, the underlying mechanisms of their biological [...] Read more.
Cannabis has been used historically for both medicinal and recreational purposes, with the most notable cannabinoids being cannabidiol (CBD) and tetrahydrocannabinol (THC). Although their therapeutic effects have been well studied and their recreational use is highly debated, the underlying mechanisms of their biological effects remain poorly defined. In this study, we use isobaric tag-based sample multiplexed proteome profiling to investigate protein abundance differences in the human neuroblastoma SH-SY5Y cell line treated with CBD and THC. We identified significantly regulated proteins by each treatment and performed a pathway classification and associated protein–protein interaction analysis. Our findings suggest that these treatments may lead to mitochondrial dysfunction and induce endoplasmic reticulum stress. These data can potentially be interrogated further to investigate the potential role of CBD and THC in various biological and disease contexts, providing a foundation for future studies. Full article
(This article belongs to the Special Issue Quantitative Proteomics: Techniques and Applications)
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13 pages, 3021 KiB  
Article
Comparative Proteomic Analysis of Two Commonly Used Laboratory Yeast Strains: W303 and BY4742
by Valentina Rossio, Xinyue Liu and Joao A. Paulo
Proteomes 2023, 11(4), 30; https://doi.org/10.3390/proteomes11040030 - 9 Oct 2023
Cited by 3 | Viewed by 2555
Abstract
The yeast Saccharomyces cerevisiae is a powerful model system that is often used to expand our understanding of cellular processes and biological functions. Although many genetically well-characterized laboratory strains of S. cerevisiae are available, they may have different genetic backgrounds which can confound [...] Read more.
The yeast Saccharomyces cerevisiae is a powerful model system that is often used to expand our understanding of cellular processes and biological functions. Although many genetically well-characterized laboratory strains of S. cerevisiae are available, they may have different genetic backgrounds which can confound data interpretation. Here, we report a comparative whole-proteome analysis of two common laboratory yeast background strains, W303 and BY4742, in both exponential and stationary growth phases using isobaric-tag-based mass spectrometry to highlight differences in proteome complexity. We quantified over 4400 proteins, hundreds of which showed differences in abundance between strains and/or growth phases. Moreover, we used proteome-wide protein abundance to profile the mating type of the strains used in the experiment, the auxotrophic markers, and associated metabolic pathways, as well as to investigate differences in particular classes of proteins, such as the pleiotropic drug resistance (PDR) proteins. This study is a valuable resource that offers insight into mechanistic differences between two common yeast background strains and can be used as a guide to select a background that is best suited for addressing a particular biological question. Full article
(This article belongs to the Special Issue Quantitative Proteomics: Techniques and Applications)
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Review

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17 pages, 575 KiB  
Review
The Current State of Proteomics and Metabolomics for Inner Ear Health and Disease
by Motahare Khorrami, Christopher Pastras, Paul A. Haynes, Mehdi Mirzaei and Mohsen Asadnia
Proteomes 2024, 12(2), 17; https://doi.org/10.3390/proteomes12020017 - 4 Jun 2024
Viewed by 1617
Abstract
Characterising inner ear disorders represents a significant challenge due to a lack of reliable experimental procedures and identified biomarkers. It is also difficult to access the complex microenvironments of the inner ear and investigate specific pathological indicators through conventional techniques. Omics technologies have [...] Read more.
Characterising inner ear disorders represents a significant challenge due to a lack of reliable experimental procedures and identified biomarkers. It is also difficult to access the complex microenvironments of the inner ear and investigate specific pathological indicators through conventional techniques. Omics technologies have the potential to play a vital role in revolutionising the diagnosis of ear disorders by providing a comprehensive understanding of biological systems at various molecular levels. These approaches reveal valuable information about biomolecular signatures within the cochlear tissue or fluids such as the perilymphatic and endolymphatic fluid. Proteomics identifies changes in protein abundance, while metabolomics explores metabolic products and pathways, aiding the characterisation and early diagnosis of diseases. Although there are different methods for identifying and quantifying biomolecules, mass spectrometry, as part of proteomics and metabolomics analysis, could be utilised as an effective instrument for understanding different inner ear disorders. This study aims to review the literature on the application of proteomic and metabolomic approaches by specifically focusing on Meniere’s disease, ototoxicity, noise-induced hearing loss, and vestibular schwannoma. Determining potential protein and metabolite biomarkers may be helpful for the diagnosis and treatment of inner ear problems. Full article
(This article belongs to the Special Issue Quantitative Proteomics: Techniques and Applications)
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Graphical abstract

20 pages, 1318 KiB  
Review
Key Proteomics Tools for Fundamental and Applied Microalgal Research
by Maxence Plouviez and Eric Dubreucq
Proteomes 2024, 12(2), 13; https://doi.org/10.3390/proteomes12020013 - 4 Apr 2024
Cited by 2 | Viewed by 2367
Abstract
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown [...] Read more.
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field. Full article
(This article belongs to the Special Issue Quantitative Proteomics: Techniques and Applications)
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