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Identification of Biomolecules by Mass Spectrometry

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 15316

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Special Issue Editors

Prof. Dr. Marek M. Kowalczuk

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Guest Editor

Centre of Polymer and Carbon Materials Polish Academy of Sciences, PL-41819 Zabrze, Poland
Interests: biocompatible and biodegradable polymer systems; polymer mass spectrometry; bioactive oligomers; controlled drug delivery systems; ring-opening polymerization; forensic engineering of advanced polymeric materials
Special Issues, Collections and Topics in MDPI journals

Dr. Anna Drabik

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Guest Editor

AGH University of Science and Technology, Krakow MP, Poland
Interests: mass spectrometry; aptamers; cancer; proteomics; neurobiology; addiction studies

Special Issue Information

Dear Collesgues,

Recent advances in mass spectrometry techniques facilitate the identification of biomolecules in very low concentrations in complex biological samples. However, there are still some limitations of the mass spectrometry approach that mainly relies on the laborious sample preparation, especially associated with the fractionation step, as well as statistical analysis of the results and the interpretation of the biological meaning of the obtained data.

This Special Issue entitled “Identification of biomolecules by mass spectrometry” will try to address those problems with relevance to biomolecules, including metabolites, hormones, peptides, proteins, oligonucleotides, nucleic acids, and bioactive compounds.

We welcome all reviews and research articles concerning the development of new methods for sample preparation, enrichment of bioanalyte fraction, experiment planning, and determination of changes in the level of potential biomarkers and their importance for mechanisms expressed in cells and living organisms.

Prof. Dr. Marek M. Kowalczuk
Dr. Anna Drabik
Guest Editors

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

mass spectrometry
biomolecules
peptides
proteins
metabolites
bioactive molecules

Published Papers (7 papers)

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Research

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15 pages, 2367 KiB

Open AccessArticle

Development of a HPLC-MS/MS Method to Assess the Pharmacokinetics and Tumour Distribution of the Dimethylarginine Dimethylaminohydrolase 1 Inhibitors ZST316 and L-257 in a Xenograft Model of Triple-Negative Breast Cancer in Mice

by Tommaso Ceruti, Roberta Frapolli, Carmen Ghilardi, Alessandra Decio, Giulia Dellavedova, Sara Tommasi, Massimo Zucchetti and Arduino A. Mangoni

Molecules 2023, 28(24), 8056; https://doi.org/10.3390/molecules28248056 - 13 Dec 2023

Cited by 1 | Viewed by 773

Abstract

We describe the development and validation of an HPLC-MS/MS method to assess the pharmacokinetics and tumour distribution of ZST316, an arginine analogue with inhibitory activity towards dimethylarginine dimethylaminohydrolase 1 (DDAH1) and vasculogenic mimicry, and its active metabolite L-257 in a xenograft model of triple-negative breast cancer (TNBC). The method proved to be reproducible, precise, and highly accurate for the measurement of both compounds in plasma and tumour tissue following acute and chronic (five days) intraperitoneal administration of ZST316 (30 mg/Kg daily) in six-week-old severe combined immunodeficiency disease (SCID) mice inoculated with MDA-MB-231 TNBC cells. ZST316 was detected in tumour tissue and plasma after 1 h (6.47 and 9.01 μM, respectively) and 24 h (0.13 and 0.16 μM, respectively) following acute administration, without accumulation during chronic treatment. Similarly, the metabolite L-257 was found in tumour tissue and plasma after 1 h (15.06 and 8.72 μM, respectively) and 24 h (0.17 and 0.17 μM, respectively) following acute administration of ZST316, without accumulation during chronic treatment. The half-life after acute and chronic treatment ranged between 4.4–7.1 h (plasma) and 4.5–5.0 h (tumour) for ZST316, and 4.2–5.3 h (plasma) and 3.6–4.9 h (tumour) for L-257. The results of our study demonstrate the (a) capacity to accurately measure ZST316 and L-257 concentrations in plasma and tumour tissue in mice using the newly developed HPLC-MS/MS method, (b) rapid conversion of ZST316 into L-257, (c) good intra-tumour penetration of both compounds, and (d) lack of accumulation of both ZST316 and L-257 in plasma and tumour tissue during chronic administration. Compared to a previous method developed by our group to investigate ZST316 in plasma, the main advantages of the new method include a wider range of linearity which reduces the need for dilutions and the combined assessment of ZST316 and L-257 in plasma and tumour tissue which limits the required amount of matrix. The new HPLC-MS/MS method is useful to investigate the in vivo effects of ZST316 and L-257 on vasculogenic mimicry, tumour mass, and metastatic burden in xenograft models of TNBC. Full article

(This article belongs to the Special Issue Identification of Biomolecules by Mass Spectrometry)

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17 pages, 2117 KiB

Open AccessArticle

Intact Transition Epitope Mapping—Serological Inspection by Epitope EXtraction (ITEM—SIX)

by Agatino Zammataro, Cornelia Koy, Manuela Ruß, Claudia Röwer and Michael O. Glocker

Molecules 2023, 28(7), 3092; https://doi.org/10.3390/molecules28073092 - 30 Mar 2023

Cited by 3 | Viewed by 1254

Abstract

Precision medicine requests accurate serological inspections to precisely stratify patients for targeted treatment. Intact transition epitope mapping analysis proved surrogate seroconversion of a model organism’s serum when spiked with a monoclonal murine anti-Ovalbumin antibody (mAb) with epitope resolution. Isolation of the IgG fraction from blood serum applied two consecutive protein precipitation steps followed by ultrafiltration and resulted in an ESI-MS analysis-ready IgG preparation. For epitope mapping by epitope extraction, the Ovalbumin antigen was digested with trypsin. After desalting, the peptide mixture was added to the ESI-MS-ready IgG preparation from mAb-spiked serum and the solution was incubated to form an immune complex between the Ovalbumin-derived epitope peptide and the anti-Ovalbumin mAb. Then, the entire mixture of proteins and peptides was directly electrosprayed. Sorting of ions in the mass spectrometer’s gas phase, dissociation of the immune complex ions by collision-induced dissociation, and recording of the epitope peptide ion that had been released from the immune complex proved the presence of the anti-Ovalbumin mAb in serum. Mass determination of the complex-released epitope peptide ion with isotope resolution is highly accurate, guaranteeing high specificity of this novel analysis approach, which is termed Intact Transition Epitope Mapping—Serological Inspections by Epitope EXtraction (ITEM—SIX). Full article

(This article belongs to the Special Issue Identification of Biomolecules by Mass Spectrometry)

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16 pages, 2251 KiB

Open AccessFeature PaperArticle

Mass Spectrometry versus Conventional Techniques of Protein Detection: Zika Virus NS3 Protease Activity towards Cellular Proteins

by Agnieszka Dabrowska, Aleksandra Milewska, Joanna Ner-Kluza, Piotr Suder and Krzysztof Pyrc

Molecules 2021, 26(12), 3732; https://doi.org/10.3390/molecules26123732 - 18 Jun 2021

Cited by 1 | Viewed by 2734

Abstract

Mass spectrometry (MS) used in proteomic approaches is able to detect hundreds of proteins in a single assay. Although undeniable high analytical power of MS, data acquired sometimes lead to confusing results, especially during a search of very selective, unique interactions in complex biological matrices. Here, we would like to show an example of such confusing data, providing an extensive discussion on the observed phenomenon. Our investigations focus on the interaction between the Zika virus NS3 protease, which is essential for virus replication. This enzyme is known for helping to remodel the microenvironment of the infected cells. Several reports show that this protease can process cellular substrates and thereby modify cellular pathways that are important for the virus. Herein, we explored some of the targets of NS3, clearly shown by proteomic techniques, as processed during infection. Unfortunately, we could not confirm the biological relevance of protein targets for viral infections detected by MS. Thus, although mass spectrometry is highly sensitive and useful in many instances, also being able to show directions where cell/virus interaction occurs, we believe that deep recognition of their biological role is essential to receive complete insight into the investigated process. Full article

(This article belongs to the Special Issue Identification of Biomolecules by Mass Spectrometry)

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11 pages, 4870 KiB

Open AccessArticle

The Study of Derivatization Prior MALDI MSI Analysis—Charge Tagging Based on the Cholesterol and Betaine Aldehyde

by Przemyslaw Mielczarek, Tymoteusz Slowik, Jolanta Helena Kotlinska, Piotr Suder and Anna Bodzon-Kulakowska

Molecules 2021, 26(9), 2737; https://doi.org/10.3390/molecules26092737 - 06 May 2021

Cited by 7 | Viewed by 2169

Abstract

Mass spectrometry imaging is a powerful tool for analyzing the different kinds of molecules in tissue sections, but some substances cannot be measured easily, due to their physicochemical properties. In such cases, chemical derivatization could be applied to introduce the charge into the molecule and facilitate its detection. Here, we study cholesterol derivatization with betaine aldehyde from tissue slices and evaluate how different sample preparation methods influence the signal from the derivatization product. In this study, we have tested different solutions for betaine aldehyde, different approaches to betaine aldehyde deposition (number of layers, deposition nozzle height), and different MALDI matrices for its analysis. As a result, we proved that the proposed approach could be used for the analysis of cholesterol in different tissues. Full article

(This article belongs to the Special Issue Identification of Biomolecules by Mass Spectrometry)

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16 pages, 4357 KiB

Open AccessArticle

MALDI MSI Reveals the Spatial Distribution of Protein Markers in Tracheobronchial Lymph Nodes and Lung of Pigs after Respiratory Infection

by Tomas Do, Roman Guran, Rea Jarosova, Petra Ondrackova, Zbysek Sladek, Martin Faldyna, Vojtech Adam and Ondrej Zitka

Molecules 2020, 25(23), 5723; https://doi.org/10.3390/molecules25235723 - 03 Dec 2020

Cited by 5 | Viewed by 2914

Abstract

Respiratory infections are a real threat for humans, and therefore the pig model is of interest for studies. As one of a case for studies, Actinobacillus pleuropneumoniae (APP) caused infections and still worries many pig breeders around the world. To better understand the influence of pathogenic effect of APP on a respiratory system—lungs and tracheobronchial lymph nodes (TBLN), we aimed to employ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry imaging (MALDI-TOF MSI). In this study, six pigs were intranasally infected by APP and two were used as non-infected control, and 48 cryosections have been obtained. MALDI-TOF MSI and immunohistochemistry (IHC) were used to study spatial distribution of infectious markers, especially interleukins, in cryosections of porcine tissues of lungs (necrotic area, marginal zone) and tracheobronchial lymph nodes (TBLN) from pigs infected by APP. CD163, interleukin 1β (IL-1β) and a protegrin-4 precursor were successfully detected based on their tryptic fragments. CD163 and IL-1β were confirmed also by IHC. The protegrin-4 precursor was identified by MALDI-TOF/TOF directly on the tissue cryosections. CD163, IL-1β and protegrin-4 precursor were all significantly (p < 0.001) more expressed in necrotic areas of lungs infected by APP than in marginal zone, TBLN and in control lungs. Full article

(This article belongs to the Special Issue Identification of Biomolecules by Mass Spectrometry)

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Review

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34 pages, 6949 KiB

Open AccessReview

Mass Spectrometry of Esterified Cyclodextrins

by Diana-Andreea Blaj, Marek Kowalczuk and Cristian Peptu

Molecules 2023, 28(5), 2001; https://doi.org/10.3390/molecules28052001 - 21 Feb 2023

Cited by 2 | Viewed by 2215

Abstract

Cyclodextrins are cyclic oligosaccharides that have received special attention due to their cavity-based structural architecture that imbues them with outstanding properties, primarily related to their capacity to host various guest molecules, from low-molecular-mass compounds to polymers. Cyclodextrin derivatization has been always accompanied by the development of characterization methods, able to unfold complicated structures with increasing precision. One of the important leaps forward is represented by mass spectrometry techniques with soft ionization, mainly matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). In this context, esterified cyclodextrins (ECDs) benefited also from the formidable input of structural knowledge, thus allowing the understanding of the structural impact of reaction parameters on the obtained products, especially for the ring-opening oligomerization of cyclic esters. The current review envisages the common mass spectrometry approaches such as direct MALDI MS or ESI MS analysis, hyphenated liquid chromatography-mass spectrometry, and tandem mass spectrometry, employed for unraveling the structural features and particular processes associated with ECDs. Thus, the accurate description of complex architectures, advances in the gas phase fragmentation processes, assessment of secondary reactions, and reaction kinetics are discussed in addition to typical molecular mass measurements. Full article

(This article belongs to the Special Issue Identification of Biomolecules by Mass Spectrometry)

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16 pages, 1641 KiB

Open AccessReview

Hemorphins—From Discovery to Functions and Pharmacology

by Przemyslaw Mielczarek, Kinga Hartman, Anna Drabik, Hao-Yuan Hung, Eagle Yi-Kung Huang, Ewa Gibula-Tarlowska, Jolanta H. Kotlinska and Jerzy Silberring

Molecules 2021, 26(13), 3879; https://doi.org/10.3390/molecules26133879 - 25 Jun 2021

Cited by 15 | Viewed by 2207

Abstract

During the last three decades, a variety of different studies on bioactive peptides that are opioid receptor ligands, have been carried out, with regard to their isolation and identification, as well as their molecular functions in living organisms. Thus, in this review, we would like to summarize the present state-of-the art concerning hemorphins, methodological aspects of their identification, and their potential role as therapeutic agents. We have collected and discussed articles describing hemorphins, from their discovery up until now, thus presenting a very wide spectrum of their characteristic and applications. One of the major assets of the present paper is a combination of analytical and pharmacological aspects of peptides described by a team who participated in the initial research on hemorphins. This review is, in part, focused on the analysis of endogenous opioid peptides in biological samples using advanced techniques, description of the identification of synthetic/endogenous hemorphins, their involvement in pharmacology, learning, pain and other function. Finally, the part regarding hemorphin analogues and their synthesis, has been added. Full article

(This article belongs to the Special Issue Identification of Biomolecules by Mass Spectrometry)

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