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Quantitative Mass Spectrometry of Small Molecules to Proteins

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 16657

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Dr. C. Michael Greenlief

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College of Arts and Science, University of Missouri, 125 Chemistry Bldg., Columbia, MO 65211, USA
Interests: biological mass spectrometry; separation of complex mixtures; quantitative proteomics; directed metabolite analysis
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Special Issue Information

Dear Colleagues,

The use of mass spectrometry to help elucidate chemical systems has grown significantly in recent years. Often coupled with chromatography, quantitative measurements can be achieved in a surprising number of systems. Mass spectrometry-based analyses can examine small molecules used drug discovery to mapping of metabolomes and proteomes. Directed analysis can obtain quantitative results in complex matrices. The goal of this special issue is to explore the wide variety of systems that can be explored by quantitative mass spectrometry.

Dr. C. Michael Greenlief
Guest Editor

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Keywords

quantitative mass spectrometry
chromatographic separations
small molecule mass spectrometry
proteomics
metabolomics

Published Papers (7 papers)

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Research

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12 pages, 1170 KiB

Open AccessArticle

Confirmation of Statin and Fibrate Use from Small-Volume Archived Plasma Samples by High-Throughput LC-MS/MS Method

by Jennifer D. Kusovschi, Anna A. Ivanova, Michael S. Gardner, Robert W. McGarrah III, William E. Kraus, Zsuzsanna Kuklenyik, James L. Pirkle and John R. Barr

Int. J. Mol. Sci. 2023, 24(9), 7931; https://doi.org/10.3390/ijms24097931 - 27 Apr 2023

Cited by 1 | Viewed by 1267

Abstract

Designing studies for lipid-metabolism-related biomarker discovery is challenging because of the high prevalence of various statin and fibrate usage for lipid-lowering therapies. When the statin and fibrate use is determined based on self-reports, patient adherence to the prescribed statin dose regimen remains unknown. A potentially more accurate way to verify a patient’s medication adherence is by direct analytical measurements. Current analytical methods are prohibitive because of the limited panel of drugs per test and large sample volume requirement that is not available from archived samples. A 4-min-long method was developed for the detection of seven statins and three fibrates using 10 µL of plasma analyzed via reverse-phase liquid chromatography and tandem mass spectrometry. The method was applied to the analysis of 941 archived plasma samples collected from patients before cardiac catheterization. When statin use was self-reported, statins were detected in 78.6% of the samples. In the case of self-reported atorvastatin use, the agreement with detection was 90.2%. However, when no statin use was reported, 42.4% of the samples had detectable levels of statins, with a similar range of concentrations as the samples from the self-reported statin users. The method is highly applicable in population studies designed for biomarker discovery or diet and lifestyle intervention studies, where the accuracy of statin or fibrate use may strongly affect the statistical evaluation of the biomarker data. Full article

(This article belongs to the Special Issue Quantitative Mass Spectrometry of Small Molecules to Proteins)

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35 pages, 3905 KiB

Open AccessArticle

Design and Validation of a Sensitive Multisteroid LC-MS/MS Assay for the Routine Clinical Use: One-Step Sample Preparation with Phospholipid Removal and Comparison to Immunoassays

by Valentin Braun, Hermann Stuppner, Lorenz Risch and Christoph Seger

Int. J. Mol. Sci. 2022, 23(23), 14691; https://doi.org/10.3390/ijms232314691 - 24 Nov 2022

Cited by 3 | Viewed by 2479

Abstract

Steroid analysis in clinical laboratories is dominated by immunoassays (IAs) that have a high sample turnover but are inherently limited in trueness, precision, and sensitivity. Liquid chromatography coupled to mass spectrometry (LC-MS/MS) has proved to be a far more capable tool, delivering better sensitivity, specificity, and the possibility of parallel analysis of multiple steroids and metabolites, providing the endocrinologist with more reliable and comprehensive diagnostic information. An LC-MS/MS assay with gradient elution over less than eight minutes and a one-step sample preparation combining protein precipitation with phospholipid removal of off-line solid-phase extraction was developed and validated. It allowed the quantification of 11-deoxycorticosterone (11-DOC), 11-deoxycortisol (11-DF), 17-OH-progesterone (17P), 21-deoxycortisol (21-DF), androstenedione (ANDRO), aldosterone (ALDO), corticosterone (CC), cortisol (CL), cortisone (CN), dehydroepiandrosterone (DHEA), dehydroepiandrosterone sulfate (DHEAS), dihydrotestosterone (DHT), estradiol (E2), progesterone (PROG), and testosterone (TES) in human serum. Interday imprecision was generally better than 15%, trueness was proven by recovery experiments with ISO 17034-certified reference materials, proficiency testing (UK NEQAS), and measuring serum reference standards. In-house comparison against IVD-CE-certified immunoassays (IA) for 17P, ANDRO, CL, DHEAS, E2, PROG, and TES was conducted by assessing leftover routine patient samples and purpose-built patient serum pools. None of the compared routine IAs were meeting the standards of the LC-MS/MS. Insufficient overall comparability was found for ANDRO and 17P (mean bias > +65%). Accuracy limitations at lower concentrations were present in IAs for PROG, E2, and TES. Full article

(This article belongs to the Special Issue Quantitative Mass Spectrometry of Small Molecules to Proteins)

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18 pages, 2400 KiB

Open AccessArticle

Simultaneous Degradation Study of Isomers in Human Plasma by HPLC-MS/MS and Application of LEDA Algorithm for Their Characterization

by Marco Pallecchi, Laura Braconi, Marta Menicatti, Sara Giachetti, Silvia Dei, Elisabetta Teodori and Gianluca Bartolucci

Int. J. Mol. Sci. 2022, 23(21), 13139; https://doi.org/10.3390/ijms232113139 - 28 Oct 2022

Cited by 5 | Viewed by 1095

Abstract

This paper proposes a tandem mass spectrometry (MS/MS) approach in isomer recognition by playing in the “energetic dimension” of the experiment. The chromatographic set up (HPLC) was tuned to minimize the run time, without requiring high efficiency or resolution between the isomers. Then, the MS/MS properties were explored to solve the signal assignment by performing a series of energy resolved experiments in order to optimize the parameters, and by applying an interesting post-processing data elaboration tool (LEDA). The reliability of the new approach was evaluated, determining the accuracy and precision of the quantitative results through analysis of the isomer mixture solutions. Next, the proposed method was applied in a chemical stability study of human plasma samples through the simultaneous addition of a pair of isomers. In the studied case, only one of the isomers suffered of enzymatic hydrolysis; therefore, the influence of the stable isomer on the degradation rate of the other was verified. In order to monitor this process correctly, it must be possible to distinguish each isomer present in the sample, quantify it, and plot its degradation profile. The reported results demonstrated the effectiveness of the LEDA algorithm in separating the isomers, without chromatographic resolution, and monitoring their behavior in human plasma samples. Full article

(This article belongs to the Special Issue Quantitative Mass Spectrometry of Small Molecules to Proteins)

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16 pages, 1318 KiB

Open AccessArticle

Multi-Omics Reveals Mechanisms of Partial Modulation of COVID-19 Dysregulation by Glucocorticoid Treatment

by Matt Spick, Amy Campbell, Ivona Baricevic-Jones, Johanna von Gerichten, Holly-May Lewis, Cecile F. Frampas, Katie Longman, Alexander Stewart, Deborah Dunn-Walters, Debra J. Skene, Nophar Geifman, Anthony D. Whetton and Melanie J. Bailey

Int. J. Mol. Sci. 2022, 23(20), 12079; https://doi.org/10.3390/ijms232012079 - 11 Oct 2022

Cited by 12 | Viewed by 2266

Abstract

Treatments for COVID-19 infections have improved dramatically since the beginning of the pandemic, and glucocorticoids have been a key tool in improving mortality rates. The UK’s National Institute for Health and Care Excellence guidance is for treatment to be targeted only at those requiring oxygen supplementation, however, and the interactions between glucocorticoids and COVID-19 are not completely understood. In this work, a multi-omic analysis of 98 inpatient-recruited participants was performed by quantitative metabolomics (using targeted liquid chromatography-mass spectrometry) and data-independent acquisition proteomics. Both ‘omics datasets were analysed for statistically significant features and pathways differentiating participants whose treatment regimens did or did not include glucocorticoids. Metabolomic differences in glucocorticoid-treated patients included the modulation of cortisol and bile acid concentrations in serum, but no alleviation of serum dyslipidemia or increased amino acid concentrations (including tyrosine and arginine) in the glucocorticoid-treated cohort relative to the untreated cohort. Proteomic pathway analysis indicated neutrophil and platelet degranulation as influenced by glucocorticoid treatment. These results are in keeping with the key role of platelet-associated pathways and neutrophils in COVID-19 pathogenesis and provide opportunity for further understanding of glucocorticoid action. The findings also, however, highlight that glucocorticoids are not fully effective across the wide range of ‘omics dysregulation caused by COVID-19 infections. Full article

(This article belongs to the Special Issue Quantitative Mass Spectrometry of Small Molecules to Proteins)

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17 pages, 9178 KiB

Open AccessArticle

Lipidomics for Determining Giant Panda Responses in Serum and Feces Following Exposure to Different Amount of Bamboo Shoot Consumption: A First Step towards Lipidomic Atlas of Bamboo, Giant Panda Serum and Feces by Means of GC-MS and UHPLC-HRMS/MS

by Chenglin Zhu, Xin Pan, Guo Li, Caiwu Li, Daifu Wu, Junni Tang, Yan Huang, Likou Zou and Luca Laghi

Int. J. Mol. Sci. 2022, 23(19), 11544; https://doi.org/10.3390/ijms231911544 - 29 Sep 2022

Cited by 2 | Viewed by 1707

Abstract

Lipidic metabolites play essential roles in host physiological health and growth performance, serving as the major structural and signaling components of membranes, energy storage molecules, and steroid hormones. Bamboo, as wild giant pandas’ exclusive diet, is the main determinant of giant pandas’ lipidome, both as a direct source and through microbiota activity. Interestingly, the consumption of bamboo has attracted little attention from a lipidomic perspective. In the current study, we outline the lipidomic atlas of different parts of bamboo. By gas chromatography—mass spectrometry (GC-MS), we have been able to obtain the absolute quantification of 35 fatty acids pertaining to short chain fatty acids (8), medium chain fatty acids (6), long chain fatty acids (17), and very long chain fatty acids (4), while liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS/MS) allowed us to obtain the relative quantification of another 1638 lipids. Among the fatty acids quantified in absolute terms, eight showed significantly distinct concentrations among different bamboo parts. Subsequently, we investigated how the giant panda’s serum and fecal lipidome adapt to the most important annual change in their diet, represented by the consumption of high amounts of bamboo shoots, typical of spring, the weight-gaining season. Five fatty acids were significantly altered in feces and two in serum, respectively, due to the different levels of bamboo shoot consumption. Furthermore, significant differences of the main bacteria strains were observed in feces between the two groups at the genus level, pertaining to Streptococcus, Leuconostoc, and Vagococcus. Correlations between giant panda fecal microbiome and lipidome were evaluated by Pearson correlation analysis. These findings suggest that a balanced diet, important for the overall lipidomic function and giant panda health, could be reached even in this remarkable case of a single food-based diet, by administering to the giant panda’s combinations of different parts of bamboo, with specific lipidome profiles. Full article

(This article belongs to the Special Issue Quantitative Mass Spectrometry of Small Molecules to Proteins)

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Review

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20 pages, 3671 KiB

Open AccessReview

Bioanalysis of Oligonucleotide by LC–MS: Effects of Ion Pairing Regents and Recent Advances in Ion-Pairing-Free Analytical Strategies

by Aowen Liu, Ming Cheng, Yixuan Zhou and Pan Deng

Int. J. Mol. Sci. 2022, 23(24), 15474; https://doi.org/10.3390/ijms232415474 - 07 Dec 2022

Cited by 6 | Viewed by 4669

Abstract

Oligonucleotides (OGNs) are relatively new modalities that offer unique opportunities to expand the therapeutic targets. Reliable and high-throughput bioanalytical methods are pivotal for preclinical and clinical investigations of therapeutic OGNs. Liquid chromatography–mass spectrometry (LC–MS) is now evolving into being the method of choice for the bioanalysis of OGNs. Ion paring reversed-phase liquid chromatography (IP-RPLC) has been widely used in sample preparation and LC–MS analysis of OGNs; however, there are technical issues associated with these methods. IP-free methods, such as hydrophilic interaction liquid chromatography (HILIC) and anion-exchange techniques, have emerged as promising approaches for the bioanalysis of OGNs. In this review, the state-of-the-art IP-RPLC–MS bioanalytical methods of OGNs and their metabolites published in the past 10 years (2012–2022) are critically reviewed. Recent advances in IP-reagent-free LC–MS bioanalysis methods are discussed. Finally, we describe future opportunities for developing new methods that can be used for the comprehensive bioanalysis of OGNs. Full article

(This article belongs to the Special Issue Quantitative Mass Spectrometry of Small Molecules to Proteins)

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29 pages, 2292 KiB

Open AccessReview

Indirect Enantioseparations: Recent Advances in Chiral Metabolomics for Biomedical Research

by Luisa-Gabriela Bogos, Ioana-Ecaterina Pralea, Radu-Cristian Moldovan and Cristina-Adela Iuga

Int. J. Mol. Sci. 2022, 23(13), 7428; https://doi.org/10.3390/ijms23137428 - 04 Jul 2022

Cited by 6 | Viewed by 2355

Abstract

Chiral metabolomics is starting to become a well-defined research field, powered by the recent advances in separation techniques. This review aimed to cover the most relevant advances in indirect enantioseparations of endogenous metabolites that were published over the last 10 years, including improvements and development of new chiral derivatizing agents, along with advances in separation methodologies. Moreover, special emphasis is put on exciting advances in separation techniques combined with mass spectrometry, such as chiral discrimination by ion-mobility mass spectrometry together with untargeted strategies for profiling of chiral metabolites in complex matrices. These advances signify a leap in chiral metabolomics technologies that will surely offer a solid base to better understand the specific roles of enantiomeric metabolites in systems biology. Full article

(This article belongs to the Special Issue Quantitative Mass Spectrometry of Small Molecules to Proteins)

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