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Tandem Mass Spectrometry: Techniques and Applications

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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 March 2023) | Viewed by 53436

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Special Issue Editor

Prof. Dr. Alina Diana Zamfir

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Guest Editor

National Institute for R&D in Electrochemistry and Condensed Matter, 300569 Timisoara, Romania
Interests: biomedical mass spectrometry; glycomics; proteomics; microfluidics; biomarker discovery; structural analysis

Special Issue Information

Dear Colleagues,

The Special Issue, titled Tandem Mass Spectrometry: Techniques and Applications, will be focused on the latest achievements in development of various mass spectrometric techniques for efficient ion fragmentation in tandem (MS/MS) or multistage (MSⁿ) and their applications. Original or review articles related to novel methods or improved protocols for MSⁿ, with either regular sample infusion by electrospray (ESI); nanoESI; matrix-assisted laser desorption/ionization (MALDI); or in combination with modern microfluidics systems and powerful separation techniques, such as liquid chromatography (LC-MS/MS), capillary electrophoresis (CE-MS/MS), mono- and two-dimensional gel electrophoresis, ion mobility (IMS-MS/MS), thin layer chromatography (TLC), size-exclusion chromatography (SEC), etc., are highly welcome. A considerable part of the Special Issue will be dedicated to different applications of MSⁿ for: a) structural analysis of biomolecules such as peptides, proteins, lipids, oligo- and polysaccharides, glycoconjugates and oligonucleotides as well as small molecules; b) characterization of molecular interactions; c) development of computational methods for molecular structure elucidation and molecular modeling; and d) development of novel software tools for the interpretation of fragmentation mass spectra.

70th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics
June 5–9, 2022
Minneapolis Convention Center | Minneapolis, Minnesota
https://www.asms.org/conferences/annual-conference/annual-conference-homepage

The ASMS conference is an annual meeting organized by the American Society for Mass Spectrometry. It was formed in 1969 to promote and disseminate knowledge of mass spectrometry and allied topics. Currently, its members include over 8,500 scientists involved in research and development. Members come from academic, industrial and governmental laboratories. Their interests include the advancement of techniques and instrumentation in mass spectrometry, as well as fundamental research in chemistry, geology, forensics, biological sciences and physics.

International Mass Spectrometry Conference, IMSC 2022
27th August–2nd September
Maastricht, The Netherlands
https://www.imsc2022.com/

The International Mass Spectrometry Conference is the central event in the IMSF calendar, drawing together colleagues from universities, industry and research institutions for research workshops, policy discussions and business meetings across the breadth of mass spectrometry. The IMSC2022 program targets an in-person event with many activities to strengthen our community and to further advance the professional network in mass spectrometry.

Prof. Dr. Alina Diana Zamfir
Guest Editor

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Keywords

tandem mass spectrometry
MS/MS
multistage mass spectrometry (MSn)
ion fragmentation
electrospray ionization (ESI)
matrix-assisted laser desorption/ionization (MALDI)
liquid chromatography-tandem mass spectrometry (LC-MS/MS)
capillary electrophoresis tandem mass spectrometry (CE-MS/MS)
mono- and two-dimensional gel electrophoresis
ion mobility tandem mass spectrometry (IMS-MS/MS)
peptides
proteins
lipids
oligo- and polysaccharides
glycoconjugates
oligonucleotides
small molecules
structural analysis

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Published Papers (13 papers)

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9 pages, 1288 KiB

Open AccessCommunication

Investigation of the Influence of Charge State and Collision Energy on Oligonucleotide Fragmentation by Tandem Mass Spectrometry

by Christopher Gawlig and Michael Rühl

Molecules 2023, 28(3), 1169; https://doi.org/10.3390/molecules28031169 - 25 Jan 2023

Cited by 4 | Viewed by 3188

Abstract

Due to the increasing pharmaceutical interest of oligonucleotides, for example in antisense therapy and vaccines, their analytical characterization is of fundamental importance due to their complex structure. For this purpose, mass spectrometry is a viable tool for structural studies of nucleic acids. Structural information regarding the primary sequence of a nucleic acid can reliably be gained via tandem mass spectrometry (MSMS) fragmentation. In this work, we present the characteristic fragmentation behavior of short-chain oligonucleotides (15–35 nucleotides) with respect to the collision-induced dissociation (CID) voltage used. The relationship and influence of the length of the oligonucleotide and its charge state is also discussed. The results presented here can be helpful for estimating the required fragmentation energies of short-chain oligonucleotides and their sequencing. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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34 pages, 1312 KiB

Open AccessArticle

Investigating the Function of Human Jumping Translocation Breakpoint Protein (hJTB) and Its Interacting Partners through In-Solution Proteomics of MCF7 Cells

by Madhuri Jayathirtha, Danielle Whitham, Shelby Alwine, Mary Donnelly, Anca-Narcisa Neagu and Costel C. Darie

Molecules 2022, 27(23), 8301; https://doi.org/10.3390/molecules27238301 - 28 Nov 2022

Cited by 6 | Viewed by 2579

Abstract

Human jumping translocation breakpoint (hJTB) gene is located on chromosome 1q21 and is involved in unbalanced translocation in many types of cancer. JTB protein is ubiquitously present in normal cells but it is found to be overexpressed or downregulated in various types of cancer cells, where this protein and its isoforms promote mitochondrial dysfunction, resistance to apoptosis, genomic instability, proliferation, invasion and metastasis. Hence, JTB could be a tumor biomarker for different types of cancer, such as breast cancer (BC), and could be used as a drug target for therapy. However, the functions of the protein or the pathways through which it increases cell proliferation and invasiveness of cancer cells are not well-known. Therefore, we aim to investigate the functions of JTB by using in-solution digestion-based cellular proteomics of control and upregulated and downregulated JTB protein in MCF7 breast cancer cell line, taking account that in-solution digestion-based proteomics experiments are complementary to the initial in-gel based ones. Proteomics analysis allows investigation of protein dysregulation patterns that indicate the function of the protein and its interacting partners, as well as the pathways and biological processes through which it functions. We concluded that JTB dysregulation increases the epithelial-mesenchymal transition (EMT) potential and cell proliferation, harnessing cytoskeleton organization, apical junctional complex, metabolic reprogramming, and cellular proteostasis. Deregulated JTB expression was found to be associated with several proteins involved in mitochondrial organization and function, oxidative stress (OS), apoptosis, and interferon alpha and gamma signaling. Consistent and complementary to our previous results emerged by using in-gel based proteomics of transfected MCF7 cells, JTB-related proteins that are overexpressed in this experiment suggest the development of a more aggressive phenotype and behavior for this luminal type A non-invasive/poor-invasive human BC cell line that does not usually migrate or invade compared with the highly metastatic MDA-MB-231 cells. This more aggressive phenotype of MCF7 cells related to JTB dysregulation and detected by both in-gel and in-solution proteomics could be promoted by synergistic upregulation of EMT, Mitotic spindle and Fatty acid metabolism pathways. However, in both JTB dysregulated conditions, several downregulated JTB-interacting proteins predominantly sustain antitumor activities, attenuating some of the aggressive phenotypical and behavioral traits promoted by the overexpressed JTB-related partners. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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9 pages, 817 KiB

Open AccessArticle

Determination of Genotoxic Impurity N-Nitroso-N-methyl-4-aminobutyric Acid in Four Sartan Substances through Using Liquid Chromatography–Tandem Mass Spectrometry

by Bin Xie, Dong Guo, Binliang Mai and Jun Fan

Molecules 2022, 27(21), 7498; https://doi.org/10.3390/molecules27217498 - 3 Nov 2022

Cited by 4 | Viewed by 2943

Abstract

N-nitroso-N-methyl-4-aminobutyric acid (NMBA) is the third N-nitrosamine impurity found in sartans. Herein, a sensitive and stable LC-MS/MS method with multiple reactions monitoring mode has been developed for the quantitative determination of NMBA in four sartan substances. The effective separation of NMBA and sartan substances was achieved on a C18 column under gradient elution conditions. The mass spectrometry method of the atmospheric pressure chemical ionization source and internal standard method was selected as the quantitative analysis method of NMBA. Then, this proposed LC-MS/MS analysis method was validated in terms of specificity, sensitivity, linearity, accuracy, precision and stability. Good linearity with correlation coefficient over 0.99 was obtained at the NMBA concentration of 3–45 ng/mL, and the limit of quantification was 3 ng/mL. Additionally, the recoveries of NMBA in four sartan substances ranged from 89.9% to 115.7%. The intra-day and inter-day relative standard deviation values were less than 5.0%. In conclusion, this developed determination method for NMBA through liquid chromatography–tandem mass spectrometry showed the characteristics of good sensitivity, high accuracy and precision, which will be of great help for the quantitative analysis of NMBA in sartan products. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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24 pages, 4003 KiB

Open AccessArticle

Structural Investigation of Betulinic Acid Plasma Metabolites by Tandem Mass Spectrometry

by Roxana Ghiulai, Marius Mioc, Roxana Racoviceanu, Alexandra Prodea, Andreea Milan, Dorina Coricovac, Cristina Dehelean, Ștefana Avram, Alina D. Zamfir, Cristian V. A. Munteanu, Viviana Ivan and Codruța Şoica

Molecules 2022, 27(21), 7359; https://doi.org/10.3390/molecules27217359 - 29 Oct 2022

Cited by 5 | Viewed by 1899

Abstract

Betulinic acid (BA) has been extensively studied in recent years mainly for its antiproliferative and antitumor effect in various types of cancers. Limited data are available regarding the pharmacokinetic profile of BA, particularly its metabolic transformation in vivo. In this study, we present the screening and structural investigations by ESI Orbitrap MS in the negative ion mode and CID MS/MS of phase I and phase II metabolites detected in mouse plasma after the intraperitoneal administration of a nanoemulsion containing BA in SKH 1 female mice. Obtained results indicate that the main phase I metabolic reactions that BA undergoes are monohydroxylation, dihydroxylation, oxidation and hydrogenation, while phase II reactions involved sulfation, glucuronidation and methylation. The fragmentation pathway for BA and its plasma metabolites were elucidated by sequencing of the precursor ions by CID MS MS experiments. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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15 pages, 2371 KiB

Open AccessArticle

Identification and Structural Characterization of Novel Chondroitin/Dermatan Sulfate Hexassacharide Domains in Human Decorin by Ion Mobility Tandem Mass Spectrometry

by Mirela Sarbu, Raluca Ica, Edie Sharon, David E. Clemmer and Alina D. Zamfir

Molecules 2022, 27(18), 6026; https://doi.org/10.3390/molecules27186026 - 15 Sep 2022

Cited by 3 | Viewed by 1898

Abstract

Chondroitin sulfate (CS) and dermatan sulfate (DS) are found in nature linked to proteoglycans, most often as hybrid CS/DS chains. In the extracellular matrix, where they are highly expressed, CS/DS are involved in fundamental processes and various pathologies. The structural diversity of CS/DS domains gave rise to efforts for the development of efficient analytical methods, among which is mass spectrometry (MS), one of the most resourceful techniques for the identification of novel species and their structure elucidation. In this context, we report here on the introduction of a fast, sensitive, and reliable approach based on ion mobility separation (IMS) MS and MS/MS by collision-induced dissociation (CID), for the profiling and structural analysis of CS/DS hexasaccharide domains in human embryonic kidney HEK293 cells decorin (DCN), obtained after CS/DS chain releasing by β-elimination, depolymerization using chondroitin AC I lyase, and fractionation by size-exclusion chromatography. By IMS MS, we were able to find novel CS/DS species, i.e., under- and oversulfated hexasaccharide domains in the released CS/DS chain. In the last stage of analysis, the optimized IMS CID MS/MS provided a series of diagnostic fragment ions crucial for the characterization of the misregulations, which occurred in the sulfation code of the trisulfated-4,5-Δ-GlcAGalNAc[IdoAGalNAc]₂ sequence, due to the unusual sulfation sites. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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16 pages, 3025 KiB

Open AccessArticle

A Comprehensive Analysis of Microflora and Metabolites in the Development of Ulcerative Colitis into Colorectal Cancer Based on the Lung–Gut Correlation Theory

by Qi Tang, Ran Liu, Ge Chu, Yue Wang, Haiyue Cui, Tongrui Zhang, Kaishun Bi, Peng Gao, Zonghua Song and Qing Li

Molecules 2022, 27(18), 5838; https://doi.org/10.3390/molecules27185838 - 8 Sep 2022

Cited by 7 | Viewed by 2469

Abstract

The lungs and large intestine can co-regulate inflammation and immunity through the lung–gut axis, in which the transportation of the gut microbiota and metabolites is the most important communication channel. In our previous study, not only did the composition of the gut microbiota and metabolites related to inflammation change significantly during the transition from ulcerative colitis (UC) to colorectal cancer (CRC), but the lung tissues also showed corresponding inflammatory changes, which indicated that gastrointestinal diseases can lead to pulmonary diseases. In order to elucidate the mechanisms of this lung–gut axis, metabolites in bronchoalveolar lavage fluid (BALF) and lung tissues were detected using UHPLC–Q-TOF-MS/MS technology, while microbiome characterization was performed in BALF using 16S rDNA sequencing. The levels of pulmonary metabolites changed greatly during the development of UC to CRC. Among these changes, the concentrations of linoleic acid and 7-hydroxy-3-oxocholic acid gradually increased during the development of UC to CRC. In addition, the composition of the pulmonary microbiota also changed significantly, with an increase in the Proteobacteria and an obvious decrease in the Firmicutes. These changes were consistent with our previous studies of the gut. Collectively, the microbiota and metabolites identified above might be the key markers related to lung and gut diseases, which can be used as an indication of the transition of diseases from the gut to the lung and provide a scientific basis for clinical treatment. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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19 pages, 1922 KiB

Open AccessArticle

Gangliosidome of a Human Hippocampus in Temporal Lobe Epilepsy Resolved by High-Resolution Tandem Mass Spectrometry

by Raluca Ica, Kristina Mlinac-Jerkovic, Katarina Ilic, Tomislav Sajko, Cristian V. A. Munteanu, Alina D. Zamfir and Svjetlana Kalanj-Bognar

Molecules 2022, 27(13), 4056; https://doi.org/10.3390/molecules27134056 - 23 Jun 2022

Cited by 5 | Viewed by 2125

Abstract

In this study, we developed a high-resolution tandem mass spectrometry (HR MS) approach to assess presumed changes in gangliosidome of a human hippocampus affected by temporal lobe epilepsy (TLE) in comparison with a normal hippocampus. Gangliosides, membrane glycolipids, are particularly diverse and abundant in the human brain, and participate in ion transport and modulation of neuronal excitability. Changes in structural ganglioside pattern potentially linked to TLE molecular pathogenesis have not been explored in detail. Aiming to characterize TLE-specific gangliosidome, we analyzed the native gangliosides purified from a human hippocampal tissue sample affected by TLE and a control hippocampus using HR MS. Marked differences of ganglioside expression were shown in TLE vs. control, particularly with respect to the sialylation degree of components, discovered as a characteristic feature of TLE. Another major finding is the occurrence of tetrasialofucogangliosides in TLE and species modified by either O-acetylation or CH₃COO⁻. Structural analysis by higher-energy collisional dissociation (HCD) MS/MS gave rise to fragmentation patterns implying that the GQ1b (d18:1/18:0) isomer is specifically associated with TLE. Further investigation in a larger sample is needed in order to confirm the discovery of ganglioside structures specifically expressed in human TLE and to provide information on the probable role of gangliosides in the molecular events underlying seizures. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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17 pages, 4136 KiB

Open AccessArticle

Metabolite Identification of a Novel Anti-Leishmanial Agent OJT007 in Rat Liver Microsomes Using LC-MS/MS

by Maria Eugenia Rincon Nigro, Ting Du, Song Gao, Manvir Kaur, Huan Xie, Omonike Arike Olaleye and Dong Liang

Molecules 2022, 27(9), 2854; https://doi.org/10.3390/molecules27092854 - 30 Apr 2022

Cited by 5 | Viewed by 2469

Abstract

The purpose of this study was to identify potential metabolic pathways and metabolites of OJT007, a methionine aminopeptidase 1 (MetAP1) inhibitor. OJT007 is a novel drug with potent antiproliferative effects against Leishmania Major. We conducted in vitro Phase I oxidation and Phase II glucuronidation assays on OJT007 using rat liver microsomes. Four unknown metabolites were initially identified using a UPLC-UV system from microsomal incubated samples. LC-MS/MS analysis was then used to identify the structural characteristics of these metabolites via precursor ion scan, neutral loss scan, and product ion scan. A glucuronide metabolite was further confirmed by β-glucuronidase hydrolysis. The kinetic parameters of OJT007 glucuronidation demonstrated that OJT007 undergoes rapid metabolism. These results demonstrate the liver’s microsomal ability to mediate three mono-oxidated metabolites and one mono-glucuronide metabolite. This suggests hepatic glucuronidation metabolism of OJT007 may be the cause of its poor oral bioavailability. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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17 pages, 3346 KiB

Open AccessArticle

High-Resolution Tandem Mass Spectrometry Identifies a Particular Ganglioside Pattern in Early Diabetic Kidney Disease of Type 2 Diabetes Mellitus Patients

by Anca Suteanu-Simulescu, Alina Diana Zamfir, Raluca Ica, Mirela Sarbu, Cristian V. A. Munteanu, Florica Gadalean, Adrian Vlad, Flaviu Bob, Dragos Catalin Jianu and Ligia Petrica

Molecules 2022, 27(9), 2679; https://doi.org/10.3390/molecules27092679 - 21 Apr 2022

Cited by 2 | Viewed by 1998

Abstract

Considering the valuable information provided by glycosphingolipids as molecular markers and the limited data available for their detection and characterization in patients suffering from Type 2 diabetic kidney disease (DKD), we developed and implemented a superior method based on high-resolution (HR) mass spectrometry (MS) and tandem MS (MS/MS) for the determination of gangliosides in the urine of DKD patients. This study was focused on: (i) testing of the HR MS and MS/MS feasibility and performances in mapping and sequencing of renal gangliosides in Type 2 DM patients; (ii) determination of the changes in the urine gangliosidome of DKD patients in different stages of the disease—normo-, micro-, and macroalbuminuria—in a comparative assay with healthy controls. Due to the high resolution and mass accuracy, the comparative MS screening revealed that the sialylation status of the ganglioside components; their modification by O-acetyl, CH₃COO⁻, O-fucosyl, and O-GalNAc; as well as the composition of the ceramide represent possible markers for early DKD detection, the assessment of disease progression, and follow-up treatment. Moreover, structural investigation by MS/MS demonstrated that GQ1d(d18:1/18:0), GT1α(d18:1/18:0) and GT1b(d18:1/18:0) isomers are associated with macroalbuminuria, meriting further investigation in relation to their role in DKD. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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10 pages, 752 KiB

Open AccessArticle

Simultaneous Analysis for Quality Control of Traditional Herbal Medicine, Gungha-Tang, Using Liquid Chromatography–Tandem Mass Spectrometry

by Chang-Seob Seo and Hyeun-Kyoo Shin

Molecules 2022, 27(4), 1223; https://doi.org/10.3390/molecules27041223 - 11 Feb 2022

Cited by 10 | Viewed by 3207

Abstract

Gungha-tang (GHT), a traditional herbal medicine, consists of nine medicinal herbs (Cnidii Rhizoma, Pinelliae Tuber, Poria Sclerotium, Citri Unshius Pericarpium, Citri Unshius Pericarpium Immaturus, Aurantii Fructus Immaturus, Atracylodis Rhizoma Alba, Glycyrrhizae Radix et Rhizoma, and Zingiberis Rhizoma Recens). It has been used for various diseases caused by phlegm. This study aimed to develop and verify the simultaneous liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis method, using nine marker components (liquiritin apioside, neoeriocitrin, narirutin, naringin, hesperidin, neohesperidin, liquiritigenin, glycyrrhizin, and 6-shogaol) for quality control of GHT. LC–MS/MS analysis was conducted using a Waters TQ-XS system. All marker analytes were separated on a Waters Acquity UPLC BEH C₁₈ column (2.1 × 100 mm, 1.7 μm) using gradient elution with a distilled water solution (containing 5 mM ammonium formate and 0.1% [v/v] formic acid)–acetonitrile mobile phase. LC–MS/MS multiple reaction monitoring (MRM) analysis was carried out in negative and positive ion modes of an electrospray ionization source. The developed LC–MS/MS MRM method was validated by examining the linearity, limits of detection and quantification, recovery, and precision. LOD and LOQ values of nine markers were calculated as 0.02–8.33 ng/mL and 0.05–25.00 ng/mL. The recovery was determined to be 89.00–118.08% and precision was assessed with a coefficient of variation value of 1.74–8.64%. In the established LC–MS/MS MRM method, all markers in GHT samples were detected at 0.003–16.157 mg/g. Information gathered during the development and verification of the LC–MS/MS method will be useful for the quality assessment of GHT and other herbal medicines. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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13 pages, 1557 KiB

Open AccessArticle

Ion Mobility Mass Spectrometry Reveals Rare Sialylated Glycosphingolipid Structures in Human Cerebrospinal Fluid

by Mirela Sarbu, Dragana Fabris, Željka Vukelić, David E. Clemmer and Alina D. Zamfir

Molecules 2022, 27(3), 743; https://doi.org/10.3390/molecules27030743 - 24 Jan 2022

Cited by 11 | Viewed by 3084

Abstract

Gangliosides (GGs) represent an important class of biomolecules associated with the central nervous system (CNS). In view of their special role at a CNS level, GGs are valuable diagnostic markers and prospective therapeutic agents. By ion mobility separation mass spectrometry (IMS MS), recently implemented by us in the investigation of human CNS gangliosidome, we previously discovered a similarity between GG profiles in CSF and the brain. Based on these findings, we developed IMS tandem MS (MS/MS) to characterize rare human CSF glycoforms, with a potential biomarker role. To investigate the oligosaccharide and ceramide structures, the ions detected following IMS MS separation were submitted to structural analysis by collision-induced dissociation (CID) MS/MS in the transfer cell. The IMS evidence on only one mobility feature, together with the diagnostic fragment ions, allowed the unequivocal identification of isomers in the CSF. Hence, by IMS MS/MS, GalNAc-GD1c(d18:1/18:1) and GalNAc-GD1c(d18:1/18:0) having both Neu5Ac residues and GalNAc attached to the external galactose were for the first time discovered and structurally characterized. The present results demonstrate the high potential of IMS MS/MS for biomarker discovery and characterization in body fluids, and the perspectives of method implementation in clinical analyses targeting the early diagnosis of CNS diseases through molecular fingerprints. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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Review

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23 pages, 3834 KiB

Open AccessReview

Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research

by Laura Darie-Ion, Danielle Whitham, Madhuri Jayathirtha, Yashveen Rai, Anca-Narcisa Neagu, Costel C. Darie and Brînduşa Alina Petre

Molecules 2022, 27(19), 6196; https://doi.org/10.3390/molecules27196196 - 21 Sep 2022

Cited by 29 | Viewed by 5860

Abstract

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein–protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide “molecular pictures”, which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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29 pages, 1686 KiB

Open AccessReview

Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research

by Anca-Narcisa Neagu, Madhuri Jayathirtha, Emma Baxter, Mary Donnelly, Brindusa Alina Petre and Costel C. Darie

Molecules 2022, 27(8), 2411; https://doi.org/10.3390/molecules27082411 - 8 Apr 2022

Cited by 49 | Viewed by 17399

Abstract

Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy. Full article

(This article belongs to the Special Issue Tandem Mass Spectrometry: Techniques and Applications)

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