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Molecules
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Advancements in Proteomics: Identification and Application
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Advancements in Proteomics: Identification and Application

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

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 6799

Special Issue Editor

Dr. Ravi Gupta

E-Mail Website
Guest Editor
Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi, Delhi 110062, India
Interests: plant stress physiology; plant-pathogen interaction; plant proteomics

Special Issue Information

Dear Colleagues,

Proteomics technologies are progressing at a rapid pace and the last decade, in particular, has witnessed a huge advancement in mass spectrometry and data analysis tools. The development of data-(in)dependent acquisition, isobaric mass tags, label-free quantitation, and targeted proteomics approaches has provided a platform for the in-depth proteome analysis of different biological samples. Moreover, the development of low-protein enrichment techniques has further boosted the identification of biomarkers and other proteins which are usually not identified during whole-cell proteome analysis. In this Special Issue, articles employing gel-based and gel-free/shotgun proteomic approaches for a comparative proteome analysis, identification of post-translationally modified proteins and development of proteome maps/proteome atlases of all lifeforms are invited. 

Dr. Ravi Gupta
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

  • proteomics
  • post-translational modifications
  • isobaric mass tags
  • label-free quantitation
  • stress response
  • quantitative expression profiling
  • proteins
  • biomarkers

Published Papers (2 papers)

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Research

21 pages, 3791 KiB  
Article
Optimization and Identification of Single Mutation in Hemoglobin Variants with 2,2,2 Trifluoroethanol Modified Digestion Method and Nano−LC Coupled MALDI MS/MS
by Pushpanjali Dasauni, Nirpendra Singh, Varun Chhabra, Manoranjan Mahapatra, Renu Saxena and Suman Kundu
Molecules 2022, 27(19), 6357; https://doi.org/10.3390/molecules27196357 - 26 Sep 2022
Cited by 1 | Viewed by 2116
Abstract
Background: Hemoglobin (Hb) variants arise due to point mutations in globin chains and their pathological treatments rely heavily on the identification of the nature and location of the mutation in the globin chains. Traditional methods for diagnosis such as HPLC and electrophoresis have [...] Read more.
Background: Hemoglobin (Hb) variants arise due to point mutations in globin chains and their pathological treatments rely heavily on the identification of the nature and location of the mutation in the globin chains. Traditional methods for diagnosis such as HPLC and electrophoresis have their own limitations. Therefore, the present study aims to develop and optimize a specific method of sample processing that could lead to improved sequence coverage and analysis of Hb variants by nano LC−MALDI MS/MS. Methods: In our study, we primarily standardized various sample processing methods such as conventional digestion with trypsin followed by 10% acetonitrile treatment, digestion with multiple proteases like trypsin, Glu−C, Lys−C, and trypsin digestion subsequent to 2,2,2 trifluoroethanol (TFE) treatment. Finally, the peptides were identified by LC−MALDI MS/MS. All of these sample processing steps were primarily tested with recombinant Hb samples. After initial optimization, we found that the TFE method was the most suitable one and the efficiency of this method was applied in Hb variant identification based on high sequence coverage. Results: We developed and optimized a method using an organic solvent TFE and heat denaturation prior to digestion, resulting in 100% sequence coverage in the β−chains and 95% sequence coverage in the α−chains, which further helped in the identification of Hb mutations. A Hb variant protein sequence database was created to specify the search and reduce the search time. Conclusion: All of the mutations were identified using a bottom−up non−target approach. Therefore, a sensitive, robust and reproducible method was developed to identify single substitution mutations in the Hb variants from the sequence of the entire globin chains. Biological Significance: Over 330,000 infants are born annually with hemoglobinopathies and it is the major cause of morbidity and mortality in early childhood. Hb variants generally arise due to point mutation in the globin chains. There is high sequence homology between normal Hb and Hb variant chains. Due to this high homology between the two forms, identification of variants by mass spectrometry is very difficult and requires the full sequence coverage of α− and β−chains. As such, there is a need for a suitable method that provides 100% sequence coverage of globin chains for variant analysis by mass spectrometry. Our study provides a simple, robust, and reproducible method that is suitable for LC−MALDI and provides nearly complete sequence coverage in the globin chains. This method may be used in the near future in routine diagnosis for Hb variant analysis. Full article
(This article belongs to the Special Issue Advancements in Proteomics: Identification and Application)
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18 pages, 7199 KiB  
Article
Unravelling the Helianthus tuberosus L. (Jerusalem Artichoke, Kiku-Imo) Tuber Proteome by Label-Free Quantitative Proteomics
by Ranjith Kumar Bakku, Ravi Gupta, Cheol-Woo Min, Sun-Tae Kim, Genboku Takahashi, Junko Shibato, Seiji Shioda, Fumiko Takenoya, Ganesh Kumar Agrawal and Randeep Rakwal
Molecules 2022, 27(3), 1111; https://doi.org/10.3390/molecules27031111 - 7 Feb 2022
Cited by 7 | Viewed by 4208
Abstract
The present research investigates the tuber proteome of the ‘medicinal’ plant Jerusalem artichoke (abbreviated as JA) (Helianthus tuberosus L.) using a high-throughput proteomics technique. Although JA has been historically known to the Native Americans, it was introduced to Europe in the late [...] Read more.
The present research investigates the tuber proteome of the ‘medicinal’ plant Jerusalem artichoke (abbreviated as JA) (Helianthus tuberosus L.) using a high-throughput proteomics technique. Although JA has been historically known to the Native Americans, it was introduced to Europe in the late 19th century and later spread to Japan (referred to as ‘kiku-imo’) as a folk remedy for diabetes. Genboku Takahashi research group has been working on the cultivation and utilization of kiku-imo tuber as a traditional/alternative medicine in daily life and researched on the lowering of blood sugar level, HbA1c, etc., in human subjects (unpublished data). Understanding the protein components of the tuber may shed light on its healing properties, especially related to diabetes. Using three commercially processed JA tuber products (dried powder and dried chips) we performed total protein extraction on the powdered samples using a label-free quantitate proteomic approach (mass spectrometry) and catalogued for the first time a comprehensive protein list for the JA tuber. A total of 2967 protein groups were identified, statistically analyzed, and further categorized into different protein classes using bioinformatics techniques. We discussed the association of these proteins to health and disease regulatory metabolism. Data are available via ProteomeXchange with identifier PXD030744. Full article
(This article belongs to the Special Issue Advancements in Proteomics: Identification and Application)
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