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Proteomes
Special Issues
Targeted Analyses of Proteomes
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Targeted Analyses of Proteomes

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

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 10341

Special Issue Editor

Dr. Jörg Reinders

E-Mail Website
Guest Editor
Leibniz Research Centre for Working Environment and Human Factors, Central Unit Analytical Chemistry, Ardeystrasse 67, 44139 Dortmund, Germany
Interests: quantitative proteomics; targeted and data-independent mass spec approaches; other -omics techniques (transcriptomics, metabolomics, lipidomics, interactomics); multidimensional separations (both LC- and gel-based)

Special Issue Information

Dear Colleagues,

Proteomic studies increasingly develop from pure discovery techniques over hypothesis-generating approaches towards hypothesis-driven, targeted projects. Directed proteomic technologies which are aimed at robust and reliable quantification of a set of individual proteins or distinct protein classes are therefore in the focus of contemporary research. This Special Issue will provide an overview of targeted proteomic approaches based on various different technological approaches. Therefore, specific sample preparation, fractionation and enrichment technologies, e.g., to isolate and quantify specific groups of proteins will be presented as well as targeted and ‘semi-targeted’ mass spectrometric methods like SRM and DIA approaches capable of quantifying dozens to hundreds of even thousands of proteins in parallel. It will further provide insight into nonmass-spec-based approaches, such as protein chip arrays and multiplex immunoassays as used in many clinical studies. The Special Issue will focus on the underlying technologies and the diverse concepts which should enable researchers from different areas to use these methods for their own projects. The multitude of conceptually different, targeted proteomics technologies has established ‘targeted proteomics’ as a mighty and highly versatile tool tailorable to a variety of analytical challenges in all areas of contemporary research.

Dr. Jörg Reinders
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

  • targeted protein quantification
  • selected reaction monitoring
  • data-independent acquisition
  • enrichment strategies
  • protein arrays
  • stable-isotope labeling
  • label-free quantification
  • immunoassays
  • interactomics
  • protein complexes

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Published Papers (2 papers)

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Research

17 pages, 4747 KiB  
Article
Targeted Quantification of the Lysosomal Proteome in Complex Samples
by Peter Mosen, Anne Sanner, Jasjot Singh and Dominic Winter
Proteomes 2021, 9(1), 4; https://doi.org/10.3390/proteomes9010004 - 26 Jan 2021
Cited by 16 | Viewed by 6356
Abstract
In eukaryotic cells, lysosomes play a crucial role in the breakdown of a variety of components ranging from small molecules to complex structures, ascertaining the continuous turnover of cellular building blocks. Furthermore, they act as a regulatory hub for metabolism, being crucially involved [...] Read more.
In eukaryotic cells, lysosomes play a crucial role in the breakdown of a variety of components ranging from small molecules to complex structures, ascertaining the continuous turnover of cellular building blocks. Furthermore, they act as a regulatory hub for metabolism, being crucially involved in the regulation of major signaling pathways. Currently, ~450 lysosomal proteins can be reproducibly identified in a single cell line by mass spectrometry, most of which are low-abundant, restricting their unbiased proteomic analysis to lysosome-enriched fractions. In the current study, we applied two strategies for the targeted investigation of the lysosomal proteome in complex samples: data-independent acquisition (DIA) and parallel reaction monitoring (PRM). Using a lysosome-enriched fraction, mouse embryonic fibroblast whole cell lysate, and mouse liver whole tissue lysate, we investigated the capabilities of DIA and PRM to investigate the lysosomal proteome. While both approaches identified and quantified lysosomal proteins in all sample types, and their data largely correlated, DIA identified on average more proteins, especially for lower complex samples and longer chromatographic gradients. For the highly complex tissue sample and shorter gradients, however, PRM delivered a better performance regarding both identification and quantification of lysosomal proteins. All data are available via ProteomeXchange with identifier PXDD023278. Full article
(This article belongs to the Special Issue Targeted Analyses of Proteomes)
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9 pages, 1024 KiB  
Article
Quantitative Proteomic Analysis of Biogenesis-Based Classification for Extracellular Vesicles
by Linwen Zhang, Jeremie Parot, Vincent A. Hackley and Illarion V. Turko
Proteomes 2020, 8(4), 33; https://doi.org/10.3390/proteomes8040033 - 6 Nov 2020
Cited by 8 | Viewed by 3224
Abstract
Extracellular vesicles (EVs) are traditionally divided into two major groups: (i) large vesicles originating from plasma membrane and called microvesicles, and (ii) small vesicles originating from the endoplasmic membrane and called exosomes. However, it is increasingly clear that the actual composition of a [...] Read more.
Extracellular vesicles (EVs) are traditionally divided into two major groups: (i) large vesicles originating from plasma membrane and called microvesicles, and (ii) small vesicles originating from the endoplasmic membrane and called exosomes. However, it is increasingly clear that the actual composition of a particular EV preparation cannot be adequately described with these two simple terms and is much more complex. Since the cell membrane origin of EVs predetermines their biological functions, the understanding of EV biogenesis is important for accurate interpretation of observed results. In the present study, we propose to take advantage of selective expression of some proteins in plasma or endosomal membranes and to use these proteins as plasma membrane-specific or endosomal membrane-specific markers. We have demonstrated that a quantitative mass spectrometry analysis allows simultaneous measurement of plasma membrane-specific and endosomal membrane-specific proteins in microvesicles and exosomes obtained after differential ultracentrifugation. Before mass spectrometry analysis, we also used sonicated platelets as a model of mixed EVs and multidetector asymmetrical-flow field-flow fractionation as an analytical method to verify a possible cross contamination of obtained microvesicles and exosomes. Based on the quantitative appearance of membrane-specific protein markers in EV preparations from human plasma and from human ARPE-19 cell medium, we concluded that there is no actual size limitation and both microvesicles and exosomes can be represented by large and small vesicles. Full article
(This article belongs to the Special Issue Targeted Analyses of Proteomes)
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