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Advances in Chemical and Quantitative Proteomics
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Advances in Chemical and Quantitative Proteomics

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

Deadline for manuscript submissions: closed (1 August 2022) | Viewed by 11833

Special Issue Editor

Dr. Yue Chen

E-Mail Website
Guest Editor
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
Interests: functional proteomics; epigenetics; cell signaling; cancer biology; metabolic diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Mass spectrometry-based proteomics enables sensitive and high-throughput profiling of proteome and protein isoforms with posttranslational modifications. The application of MS-based proteomics technology in biological studies has enabled the discovery of key proteins, signaling events, and regulatory mechanisms in cellular processes and in diseases. Despite these advances, the high complexity of cellular proteome and protein isoforms still represents a daunting analytical challenge for functional proteomics analysis.

Chemical proteomics leverages the innovative development or application of chemical or enzymatic tools to introduce new chemical properties to a subproteome with functional significance. Such strategies overcome the challenge of high proteome complexity and significantly increase the sensitivity of proteomics analysis through selective labeling, enrichment, or quantification of the targeted proteome of interest.

Quantitative proteomics maps the dynamics of proteins or protein isoforms associated with specific biological processes. It includes both relative and absolute quantification strategies with isotope-labeling or label-free approaches, offering another dimension to identify key proteins or modifications underlying regulatory mechanisms of cellular functions. Advances in chemical and quantitative proteomics will lead to exciting discoveries of new biology and promote broad application of proteomics technology from basic biochemical analysis of cell signaling to clinical investigations of disease progression.

The present Special issue is dedicated to advances in technology development and biological applications in chemical and quantitative proteomics. Both original research reports and review articles are considered for publication. Studies shedding light on recent developments in analytical methodology or chemical labeling strategy in proteomics analysis are especially welcome.

Dr. Yue Chen
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. 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 2700 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

  • LCMS
  • high-resolution mass spectrometry
  • quantitative proteomics
  • chemical proteomics
  • isobaric labeling
  • SILAC
  • posttranslational modification
  • cellular signaling

Published Papers (4 papers)

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Research

17 pages, 2760 KiB  
Article
High Throughput Isolation and Data Independent Acquisition Mass Spectrometry (DIA-MS) of Urinary Extracellular Vesicles to Improve Prostate Cancer Diagnosis
by Hao Zhang, Gui-Yuan Zhang, Wei-Chao Su, Ya-Ting Chen, Yu-Feng Liu, Dong Wei, Yan-Xi Zhang, Qiu-Yi Tang, Yu-Xiang Liu, Shi-Zhi Wang, Wen-Chao Li, Anke Wesselius, Maurice P. Zeegers, Zi-Yu Zhang, Yan-Hong Gu, W. Andy Tao and Evan Yi-Wen Yu
Molecules 2022, 27(23), 8155; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27238155 - 23 Nov 2022
Cited by 3 | Viewed by 2229
Abstract
Proteomic profiling of extracellular vesicles (EVs) represents a promising approach for early detection and therapeutic monitoring of diseases such as cancer. The focus of this study was to apply robust EV isolation and subsequent data-independent acquisition mass spectrometry (DIA-MS) for urinary EV proteomics [...] Read more.
Proteomic profiling of extracellular vesicles (EVs) represents a promising approach for early detection and therapeutic monitoring of diseases such as cancer. The focus of this study was to apply robust EV isolation and subsequent data-independent acquisition mass spectrometry (DIA-MS) for urinary EV proteomics of prostate cancer and prostate inflammation patients. Urinary EVs were isolated by functionalized magnetic beads through chemical affinity on an automatic station, and EV proteins were analyzed by integrating three library-base analyses (Direct-DIA, GPF-DIA, and Fractionated DDA-base DIA) to improve the coverage and quantitation. We assessed the levels of urinary EV-associated proteins based on 40 samples consisting of 20 cases and 20 controls, where 18 EV proteins were identified to be differentiated in prostate cancer outcome, of which three (i.e., SERPINA3, LRG1, and SCGB3A1) were shown to be consistently upregulated. We also observed 6 out of the 18 (33%) EV proteins that had been developed as drug targets, while some of them showed protein-protein interactions. Moreover, the potential mechanistic pathways of 18 significantly different EV proteins were enriched in metabolic, immune, and inflammatory activities. These results showed consistency in an independent cohort with 20 participants. Using a random forest algorithm for classification assessment, including the identified EV proteins, we found that SERPINA3, LRG1, or SCGB3A1 add predictable value in addition to age, prostate size, body mass index (BMI), and prostate-specific antigen (PSA). In summary, the current study demonstrates a translational workflow to identify EV proteins as molecular markers to improve the clinical diagnosis of prostate cancer. Full article
(This article belongs to the Special Issue Advances in Chemical and Quantitative Proteomics)
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14 pages, 2601 KiB  
Article
Comparing Efficiency of Lysis Buffer Solutions and Sample Preparation Methods for Liquid Chromatography–Mass Spectrometry Analysis of Human Cells and Plasma
by Lasse Neset, Gracious Takayidza, Frode S. Berven and Maria Hernandez-Valladares
Molecules 2022, 27(11), 3390; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27113390 - 25 May 2022
Cited by 4 | Viewed by 4086
Abstract
The use of a proper sample processing methodology for maximum proteome coverage and high-quality quantitative data is an important choice to make before initiating a liquid chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing workflows for proteomics involve in-solution proteome digestion and single-pot, [...] Read more.
The use of a proper sample processing methodology for maximum proteome coverage and high-quality quantitative data is an important choice to make before initiating a liquid chromatography–mass spectrometry (LC–MS)-based proteomics study. Popular sample processing workflows for proteomics involve in-solution proteome digestion and single-pot, solid-phase-enhanced sample preparation (SP3). We tested them on both HeLa cells and human plasma samples, using lysis buffers containing SDS, or guanidinium hydrochloride. We also studied the effect of using commercially available depletion mini spin columns before SP3, to increase proteome coverage in human plasma samples. Our results show that the SP3 protocol, using either buffer, achieves the highest number of quantified proteins in both the HeLa cells and plasma samples. Moreover, the use of depletion mini spin columns before SP3 results in a two-fold increase of quantified plasma proteins. With additional fractionation, we quantified nearly 1400 proteins, and examined lower-abundance proteins involved in neurodegenerative pathways and mitochondrial metabolism. Therefore, we recommend the use of the SP3 methodology for biological sample processing, including those after depletion of high-abundance plasma proteins. Full article
(This article belongs to the Special Issue Advances in Chemical and Quantitative Proteomics)
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16 pages, 2962 KiB  
Article
Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells
by Luke Erber, Shirelle Liu, Yao Gong, Phu Tran and Yue Chen
Molecules 2022, 27(2), 484; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27020484 - 13 Jan 2022
Cited by 2 | Viewed by 1877
Abstract
Iron and oxygen deficiencies are common features in pathophysiological conditions, such as ischemia, neurological diseases, and cancer. Cellular adaptive responses to such deficiencies include repression of mitochondrial respiration, promotion of angiogenesis, and cell cycle control. We applied a systematic proteomics analysis to determine [...] Read more.
Iron and oxygen deficiencies are common features in pathophysiological conditions, such as ischemia, neurological diseases, and cancer. Cellular adaptive responses to such deficiencies include repression of mitochondrial respiration, promotion of angiogenesis, and cell cycle control. We applied a systematic proteomics analysis to determine the global proteomic changes caused by acute hypoxia and chronic and acute iron deficiency (ID) in hippocampal neuronal cells. Our analysis identified over 8600 proteins, revealing similar and differential effects of each treatment on activation and inhibition of pathways regulating neuronal development. In addition, comparative analysis of ID-induced proteomics changes in cultured cells and transcriptomic changes in the rat hippocampus identified common altered pathways, indicating specific neuronal effects. Transcription factor enrichment and correlation analysis identified key transcription factors that were activated in both cultured cells and tissue by iron deficiency, including those implicated in iron regulation, such as HIF1, NFY, and NRF1. We further identified MEF2 as a novel transcription factor whose activity was induced by ID in both HT22 proteome and rat hippocampal transcriptome, thus linking iron deficiency to MEF2-dependent cellular signaling pathways in neuronal development. Taken together, our study results identified diverse signaling networks that were differentially regulated by hypoxia and ID in neuronal cells. Full article
(This article belongs to the Special Issue Advances in Chemical and Quantitative Proteomics)
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11 pages, 2478 KiB  
Article
Identification of the Protein Glycation Sites in Human Myoglobin as Rapidly Induced by d-Ribose
by Jing-Jing Liu, Yong You, Shu-Qin Gao, Shuai Tang, Lei Chen, Ge-Bo Wen and Ying-Wu Lin
Molecules 2021, 26(19), 5829; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26195829 - 26 Sep 2021
Cited by 6 | Viewed by 2772
Abstract
Protein glycation is an important protein post-translational modification and is one of the main pathogenesis of diabetic angiopathy. Other than glycated hemoglobin, the protein glycation of other globins such as myoglobin (Mb) is less studied. The protein glycation of human Mb with ribose [...] Read more.
Protein glycation is an important protein post-translational modification and is one of the main pathogenesis of diabetic angiopathy. Other than glycated hemoglobin, the protein glycation of other globins such as myoglobin (Mb) is less studied. The protein glycation of human Mb with ribose has not been reported, and the glycation sites in the Mb remain unknown. This article reports that d-ribose undergoes rapid protein glycation of human myoglobin (HMb) at lysine residues (K34, K87, K56, and K147) on the protein surface, as identified by ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). Moreover, glycation by d-ribose at these sites slightly decreased the rate of the met heme (FeIII) in reaction with H2O2 to form a ferryl heme (FeIV=O). This study provides valuable insight into the protein glycation by d-ribose and provides a foundation for studying the structure and function of glycated heme proteins. Full article
(This article belongs to the Special Issue Advances in Chemical and Quantitative Proteomics)
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