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CZE/LC-MS-based Proteomics
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CZE/LC-MS-based Proteomics

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

Deadline for manuscript submissions: closed (31 December 2019) | Viewed by 36130

Special Issue Editor

Dr. Zhenbin Zhang

E-Mail Website
Guest Editor
Department of chemistry and biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA
Interests: study of proteome using liquid chromatogray (LC) and capillary zone electrophoresis-mass spectrometry (CZE-MS); developing microreactors and novel sample preparation methods for proteomics; single cell proteomics

Special Issue Information

Dear Colleagues,

Mass spectrometry (MS)-based proteomics has established itself as an indispensable technology to interpret the information encoded in genomes. Its plays a critical role in molecular and cellular biology, as well as systems biology, due to its ability to identify and, increasingly, precisely quantifying thousands of proteins from complex samples. Although it has achieved tremendous recent success, MS-based proteomics still faces various technical challenges. The Special Issue of Molecules, entitled “Capillary Zone Electrophoresis/Liquid Chromatography(CZE/LC)-MS-Based Proteomics”, welcomes original papers and comprehensive reviews focused on, but not limited, to the improvement of techniques related to CZE/LC-MS-based proteomics, such as novel methods for sample preparation, novel separation techniques, advancements in mass spectrometers, improved methods (software) for data acquisition and analyses, and the applications of MS-based proteomics techniques, such as the study of post-translational modifications (PTMs, e.g., phosphoproteomics, glycoproteomics, etc.) or protein–protein interactions, clinical diagnoses, host cell protein analyses, as well as single-cell proteomics. Please refer to the list of keywords for further topics.

Dr. Zhenbin Zhang
Guest Editor

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Keywords

  • Bottom up proteomics
  • Top down proteomics
  • Sample preparation
  • CZE/LC-MS
  • Post-translational modifications (e.g., phosphoproteomics, glycoproteomics, etc.)
  • Protein-protein interactions
  • Clinical diagnosis
  • Single cell proteomics
  • Data analysis tools for proteomics

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Published Papers (6 papers)

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Research

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27 pages, 3484 KiB  
Article
Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi
by Tatiana Mamontova, Alexey M. Afonin, Christian Ihling, Alena Soboleva, Elena Lukasheva, Anton S. Sulima, Oksana Y. Shtark, Gulnara A. Akhtemova, Maria N. Povydysh, Andrea Sinz, Andrej Frolov, Vladimir A. Zhukov and Igor A. Tikhonovich
Molecules 2019, 24(8), 1603; https://doi.org/10.3390/molecules24081603 - 23 Apr 2019
Cited by 32 | Viewed by 4316
Abstract
Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms—rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions [...] Read more.
Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms—rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479. Full article
(This article belongs to the Special Issue CZE/LC-MS-based Proteomics)
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14 pages, 2088 KiB  
Article
Differential Proteomics Reveals miR-155 as a Novel Indicator of Liver and Spleen Pathology in the Symptomatic Niemann-Pick Disease, Type C1 Mouse Model
by Melissa R. Pergande, Antony Cougnoux, Rathnayake A. C. Rathnayake, Forbes D. Porter and Stephanie M. Cologna
Molecules 2019, 24(5), 994; https://doi.org/10.3390/molecules24050994 - 12 Mar 2019
Cited by 11 | Viewed by 4114
Abstract
Niemann-Pick disease, type C1 (NPC1) is a rare, autosomal recessive, lipid storage disorder caused by mutations in NPC1. As a result, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system. Clinically, patients can present with splenomegaly and hepatomegaly. [...] Read more.
Niemann-Pick disease, type C1 (NPC1) is a rare, autosomal recessive, lipid storage disorder caused by mutations in NPC1. As a result, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system. Clinically, patients can present with splenomegaly and hepatomegaly. In the current study, we analyzed the differential proteome of the spleen in symptomatic Npc1−/− mice to complement previous studies focused on the differential proteome of the liver, and then evaluated biomolecules that may serve as tissue biomarkers. The proteomic analysis revealed altered pathways in NPC1 representing different functional categories including heme synthesis, cellular regulation and phosphoinositide metabolism in both tissues. Differential proteins included several activators of the ubiquitous and critical protein, Akt, a major kinase involved in multiple cellular processes. Evaluation of Akt revealed decreased expression in both the liver and spleen tissues of symptomatic Npc1−/− mice. Upstream regulation analysis also suggested that miR-155 may modulate the differences of known downstream protein targets observed in our dataset. Upon evaluation of miR-155, we observed an increased expression in the liver and decreased expression in the spleen of symptomatic Npc1−/− mice. Here, we propose that miR-155 may be a novel indicator of spleen and liver pathology in NPC1. Full article
(This article belongs to the Special Issue CZE/LC-MS-based Proteomics)
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14 pages, 3396 KiB  
Article
Phosphoproteomics of Retinoblastoma: A Pilot Study Identifies Aberrant Kinases
by Lakshmi Dhevi Nagarajha Selvan, Ravikanth Danda, Anil K. Madugundu, Vinuth N. Puttamallesh, Gajanan J. Sathe, Uma Maheswari Krishnan, Vikas Khetan, Pukhraj Rishi, Thottethodi Subrahmanya Keshava Prasad, Akhilesh Pandey, Subramanian Krishnakumar, Harsha Gowda and Sailaja V. Elchuri
Molecules 2018, 23(6), 1454; https://doi.org/10.3390/molecules23061454 - 15 Jun 2018
Cited by 11 | Viewed by 5543
Abstract
Retinoblastoma is a malignant tumour of the retina which most often occurs in children. Earlier studies on retinoblastoma have concentrated on the identification of key players in the disease and have not provided information on activated/inhibited signalling pathways. The dysregulation of protein phosphorylation [...] Read more.
Retinoblastoma is a malignant tumour of the retina which most often occurs in children. Earlier studies on retinoblastoma have concentrated on the identification of key players in the disease and have not provided information on activated/inhibited signalling pathways. The dysregulation of protein phosphorylation in cancer provides clues about the affected signalling cascades in cancer. Phosphoproteomics is an ideal tool for the study of phosphorylation changes in proteins. Hence, global phosphoproteomics of retinoblastoma (RB) was carried out to identify signalling events associated with this cancer. Over 350 proteins showed differential phosphorylation in RB compared to control retina. Our study identified stress response proteins to be hyperphosphorylated in RB which included H2A histone family member X (H2AFX) and sirtuin 1. In particular, Ser140 of H2AFX also known as gamma-H2AX was found to be hyperphosphorylated in retinoblastoma, which indicated the activation of DNA damage response pathways. We also observed the activation of anti-apoptosis in retinoblastoma compared to control. These observations showed the activation of survival pathways in retinoblastoma. The identification of hyperphosphorylated protein kinases including Bromodomain containing 4 (BRD4), Lysine deficient protein kinase 1 (WNK1), and Cyclin-dependent kinase 1 (CDK1) in RB opens new avenues for the treatment of RB. These kinases can be considered as probable therapeutic targets for RB, as small-molecule inhibitors for some of these kinases are already in clinical trials for the treatment other cancers. Full article
(This article belongs to the Special Issue CZE/LC-MS-based Proteomics)
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Review

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19 pages, 1395 KiB  
Review
Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)-Based Proteomics of Drug-Metabolizing Enzymes and Transporters
by Jiapeng Li and Hao-Jie Zhu
Molecules 2020, 25(11), 2718; https://doi.org/10.3390/molecules25112718 - 11 Jun 2020
Cited by 30 | Viewed by 7797
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples, outperforming conventional antibody-based methods in many aspects. LC-MS/MS-based proteomics studies have revealed the protein abundances of many drug-metabolizing enzymes and transporters (DMETs) in tissues relevant [...] Read more.
Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples, outperforming conventional antibody-based methods in many aspects. LC-MS/MS-based proteomics studies have revealed the protein abundances of many drug-metabolizing enzymes and transporters (DMETs) in tissues relevant to drug metabolism and disposition. Previous studies have consistently demonstrated marked interindividual variability in DMET protein expression, suggesting that varied DMET function is an important contributing factor for interindividual variability in pharmacokinetics (PK) and pharmacodynamics (PD) of medications. Moreover, differential DMET expression profiles were observed across different species and in vitro models. Therefore, caution must be exercised when extrapolating animal and in vitro DMET proteomics findings to humans. In recent years, DMET proteomics has been increasingly utilized for the development of physiologically based pharmacokinetic models, and DMET proteins have also been proposed as biomarkers for prediction of the PK and PD of the corresponding substrate drugs. In sum, despite the existence of many challenges in the analytical technology and data analysis methods of LC-MS/MS-based proteomics, DMET proteomics holds great potential to advance our understanding of PK behavior at the individual level and to optimize treatment regimens via the DMET protein biomarker-guided precision pharmacotherapy. Full article
(This article belongs to the Special Issue CZE/LC-MS-based Proteomics)
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26 pages, 2720 KiB  
Review
Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies
by Camille Lombard-Banek and John E. Schiel
Molecules 2020, 25(6), 1396; https://doi.org/10.3390/molecules25061396 - 19 Mar 2020
Cited by 12 | Viewed by 5898
Abstract
Adoptive cell therapy is an emerging anti-cancer modality, whereby the patient’s own immune cells are engineered to express T-cell receptor (TCR) or chimeric antigen receptor (CAR). CAR-T cell therapies have advanced the furthest, with recent approvals of two treatments by the Food and [...] Read more.
Adoptive cell therapy is an emerging anti-cancer modality, whereby the patient’s own immune cells are engineered to express T-cell receptor (TCR) or chimeric antigen receptor (CAR). CAR-T cell therapies have advanced the furthest, with recent approvals of two treatments by the Food and Drug Administration of Kymriah (trisagenlecleucel) and Yescarta (axicabtagene ciloleucel). Recent developments in proteomic analysis by mass spectrometry (MS) make this technology uniquely suited to enable the comprehensive identification and quantification of the relevant biochemical architecture of CAR-T cell therapies and fulfill current unmet needs for CAR-T product knowledge. These advances include improved sample preparation methods, enhanced separation technologies, and extension of MS-based proteomic to single cells. Innovative technologies such as proteomic analysis of raw material quality attributes (MQA) and final product quality attributes (PQA) may provide insights that could ultimately fuel development strategies and lead to broad implementation. Full article
(This article belongs to the Special Issue CZE/LC-MS-based Proteomics)
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21 pages, 3070 KiB  
Review
Recent Advances and New Perspectives in Capillary Electrophoresis-Mass Spectrometry for Single Cell “Omics”
by Kellen DeLaney, Christopher S. Sauer, Nhu Q. Vu and Lingjun Li
Molecules 2019, 24(1), 42; https://doi.org/10.3390/molecules24010042 - 22 Dec 2018
Cited by 35 | Viewed by 7599
Abstract
Accurate clinical therapeutics rely on understanding the metabolic responses of individual cells. However, the high level of heterogeneity between cells means that simply sampling from large populations of cells is not necessarily a reliable approximation of an individual cell’s response. As a result, [...] Read more.
Accurate clinical therapeutics rely on understanding the metabolic responses of individual cells. However, the high level of heterogeneity between cells means that simply sampling from large populations of cells is not necessarily a reliable approximation of an individual cell’s response. As a result, there have been numerous developments in the field of single-cell analysis to address this lack of knowledge. Many of these developments have focused on the coupling of capillary electrophoresis (CE), a separation technique with low sample consumption and high resolving power, and mass spectrometry (MS), a sensitive detection method for interrogating all ions in a sample in a single analysis. In recent years, there have been many notable advancements at each step of the single-cell CE-MS analysis workflow, including sampling, manipulation, separation, and MS analysis. In each of these areas, the combined improvements in analytical instrumentation and achievements of numerous researchers have served to drive the field forward to new frontiers. Consequently, notable biological discoveries have been made possible by the implementation of these methods. Although there is still room in the field for numerous further advances, researchers have effectively minimized various limitations in detection of analytes, and it is expected that there will be many more developments in the near future. Full article
(This article belongs to the Special Issue CZE/LC-MS-based Proteomics)
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