bims-mascan 2024-12-08 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2024–12–08
ten papers selected by
Giovanny Rodríguez Blanco, Uniklinikum Graz

TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.
Data-Independent Acquisition-Parallel Reaction Monitoring Acquisition Reveals Age-Dependent Alterations of the Lysosomal Proteome in a Mouse Model of Metachromatic Leukodystrophy.
Research Progress in Isotope Labeling/Tags-Based Protein Quantification and Metrology Technologies.
Systematic Identification of Microtubule Posttranslational Modification "Readers" by Quantitative Proteomics.
High-resolution targeted mass spectrometry for comprehensive quantification of sphingolipids: clinical applications and characterization of extracellular vesicles.
Rapid quantification of murine bile acids using liquid chromatography-tandem mass spectrometry.
Integration of feature-based molecular networking and high-definition data-dependent acquisition for the comprehensive multicomponent characterization of Honghua Xiaoyao Tablet.
Effective data visualization strategies in untargeted metabolomics.
Simultaneous analysis of reduced and oxidized forms of multiple biological aminothiols in cells and tissues by double derivatization combined with liquid chromatography‒mass spectrometry.
Dietary fructose enhances tumour growth indirectly via interorgan lipid transfer.

J Proteome Res. 2024 Dec 06.

TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.

Abdul Rehman Basharat, Xingzhao Xiong, Tian Xu, Yong Zang, Liangliang Sun, Xiaowen Liu.

  Top-down mass spectrometry is widely used for proteoform identification, characterization, and quantification owing to its ability to analyze intact proteoforms. In the past decade, top-down proteomics has been dominated by top-down data-dependent acquisition mass spectrometry (TD-DDA-MS), and top-down data-independent acquisition mass spectrometry (TD-DIA-MS) has not been well studied. While TD-DIA-MS produces complex multiplexed tandem mass spectrometry (MS/MS) spectra, which are challenging to confidently identify, it selects more precursor ions for MS/MS analysis and has the potential to increase proteoform identifications compared with TD-DDA-MS. Here we present TopDIA, the first software tool for proteoform identification by TD-DIA-MS. It generates demultiplexed pseudo MS/MS spectra from TD-DIA-MS data and then searches the pseudo MS/MS spectra against a protein sequence database for proteoform identification. We compared the performance of TD-DDA-MS and TD-DIA-MS using Escherichia coli K-12 MG1655 cells and demonstrated that TD-DIA-MS with TopDIA increased proteoform and protein identifications compared with TD-DDA-MS.

Keywords:  data independent acquisition; mass spectrometry; proteoform identification; top-down proteomics

DOI:  https://doi.org/10.1021/acs.jproteome.4c00293
Anal Chem. 2024 Dec 02.

Data-Independent Acquisition-Parallel Reaction Monitoring Acquisition Reveals Age-Dependent Alterations of the Lysosomal Proteome in a Mouse Model of Metachromatic Leukodystrophy.

Anne Sanner, Robert Hardt, Ulrich Matzner, Dominic Winter.

For the reproducible analysis of peptides by mass spectrometry-based proteomics, data-independent acquisition (DIA) and parallel/multiple reaction monitoring (PRM/MRM) deliver unrivalled performance with respect to sensitivity and reproducibility. Both approaches, however, come with distinct advantages and shortcomings. While DIA enables unbiased whole proteome analysis, it shows limitations with respect to dynamic range and the quantification of low-abundant proteins. PRM, on the other hand, is ideally suited to reproducibly quantify selected proteins even if they are low-abundant, but no knowledge of the remaining sample is obtained. Here, we combine both methods into a mixed DIA-PRM acquisition approach, merging their benefits while operating at reduced machine run times and needed sample amounts. We demonstrate the feasibility of DIA-PRM by merging a scheduled PRM assay for 103 peptides, representing 59 low-abundant lysosomal hydrolases, with a DIA data acquisition scheme. After benchmarking DIA-PRM with mouse embryonic fibroblast (MEF) whole cell lysates, we use the approach to investigate age-related proteomic changes in brain tissues of a mouse model of metachromatic leukodystrophy (MLD). This revealed an MLD-related progressive increase in distinct classes of lysosomal hydrolases as well as alterations of proteins related to myelin and cellular metabolism. All data are available via ProteomeXchange with PXD052313.

DOI: https://doi.org/10.1021/acs.analchem.4c04378
J Proteome Res. 2024 Dec 04.

Research Progress in Isotope Labeling/Tags-Based Protein Quantification and Metrology Technologies.

Fan Wu, Chenhuan Zhang, Rui Chen, Zhanying Chu, Bin Han, Rui Zhai.

  Advanced liquid chromatogram-mass spectrometry (LC-MS) and automated large-scale data processing have made MS-based quantitative analysis increasingly useful for research in fields such as biology, medicine, food safety, and beyond. This is because MS-based quantitative analysis can accurately and sensitively analyze thousands of proteins and peptides in a single experiment. However, the precision, coverage, complexity, and resilience of conventional quantification methods vary as a result of the modifications to the analytic environment and the physicochemical characteristics of analytes. Therefore, specially designed approaches are necessary for sample preparation. Dozens of methods have been developed and adapted for these needs based on stable isotopic labeling or isobaric tagging, each with distinct characteristics. In this review, we will summarize the leading strategies and techniques used thus far for MS-based protein quantification as well as analyze the advantages and shortcomings of different approaches. Additionally, we provide an overview of protein metrology development.

Keywords:  isobaric tagging; mass spectrometry; protein metrology; protein quantification; stable isotope labeling

DOI:  https://doi.org/10.1021/acs.jproteome.4c00713
Methods Mol Biol. 2025 ;2872 189-203

Systematic Identification of Microtubule Posttranslational Modification "Readers" by Quantitative Proteomics.

Takashi Hotta, Ryoma Ohi.

  Microtubules, dynamic polymers assembled from α, β-tubulin dimers, contribute to myriad cellular processes. This is largely attributed to microtubule-associated proteins (MAPs). How MAPs selectively bind microtubules to carry out various functions is not known. The "Tubulin Code" theory proposes that posttranslational modifications (PTMs) of microtubules serve as signs that can be read by specific MAPs, thereby conferring specific functional properties to the microtubules. In support of this hypothesis, "reader" MAPs have been identified for various tubulin PTMs, but, until recently, no systematic screening had been performed to identify readers in an unbiased manner. We addressed this by developing a reader identification pipeline that uses quantitative mass spectrometry to interrogate the microtubule proteome of cells programmed to express specific PTMs. This pipeline can be used to identify readers for any tubulin PTM from various cell types as long as the writer enzymes are known. We also provide an alternative, complementary approach to obtain modified microtubules using a generic writer enzyme in vitro.

Keywords:  Microtubule; Microtubule-associated proteins; Posttranslational modifications; Quantitative proteomics

DOI:  https://doi.org/10.1007/978-1-0716-4224-5_13
Anal Biochem. 2024 Nov 30. pii: S0003-2697(24)00276-8. [Epub ahead of print]698 115732

High-resolution targeted mass spectrometry for comprehensive quantification of sphingolipids: clinical applications and characterization of extracellular vesicles.

Thiago V D Felippe, Diana M Toro, Jonatan C S de Carvalho, Pedro Nobre-Azevedo, Luiz F M Rodrigues, Bianca T M Oliveira, Pedro V da Silva-Neto, Adriana F L Vilela, Fausto Almeida, Lúcia H Faccioli, Carlos A Sorgi.

  Sphingolipids (SL), a class of membrane lipids, play important roles in numerous biological processes. Their significant structural diversity poses challenges for accurate quantification. To address this, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has emerged as a powerful tool for sphingolipidomics, capable of profiling these lipids comprehensively. In this study, we utilized LC-MS/MS with high-resolution mass spectrometry (MRMHR) to develop a targeted method for the identification and quantification of various SL species. This method, based on validated parameters such as precursor/fragment ions (m/z) and retention time, demonstrated high sensitivity and accuracy, successfully identifying SL species across 12 distinct classes. Its open-panel design also facilitates the analysis of new SL-species targets. Notably, using this approach, we identified 40 SL species in plasma samples from COVID-19 patients, and we determined the influence of matrix metalloproteinase-3 (MMP-3) expression on the positive downstream of SL metabolism. Beyond plasma analysis, this method has potential applications in other biomedical contexts, such as extracellular vesicles (EVs), describing the cargo of sphingosine-1-phosphate (S1P) on macrophage-derived EVs. The establishment of this targeted workflow enabling precise quantification of a wide range of SL species, holds promise for identifying novel biomarkers and therapeutic targets.

Keywords:  COVID-19; Extracellular vesicles; LC-MS/MS; Sphingolipids

DOI:  https://doi.org/10.1016/j.ab.2024.115732
Anal Bioanal Chem. 2024 Dec 02.

Rapid quantification of murine bile acids using liquid chromatography-tandem mass spectrometry.

Sven Hermeling, Johannes Plagge, Sabrina Krautbauer, Josef Ecker, Ralph Burkhardt, Gerhard Liebisch.

  Interest in bile acids (BAs) is growing due to their emerging role as signaling molecules and their association with various diseases such as colon cancer and metabolic syndrome. Analyzing BAs requires chromatographic separation of isomers, often with long run times, which hinders BA analysis in large studies. Here, we present a high-throughput method based on liquid chromatography-tandem mass spectrometry to quantify BAs in mouse samples. After acidic protein precipitation in the presence of a comprehensive mixture of stable isotope-labeled internal standards (SIL-ISs), BAs are separated on a biphenyl column by gradient elution at basic pH. Quantification is performed using a six-point calibration curve. Except for the separation of β- and ω-muricholic acid (MCA) species, a rapid separation of 27 BA species was achieved in a run time of 6.5 min. Plasma quality controls (QCs) were used to evaluate intra- and inter-day precision. The CV was less than 10% for most BA species and exceeded 20% only for glycohyodeoxycholic (GHDCA) and taurohyodeoxycholic acid (THDCA) due to the lack of a corresponding SIL-IS. The limit of quantification (LoQ) was tested using diluted QCs and was found to be compromised for some BA species as a result of insufficient isotopic purity of the SIL-IS, leading to significant interference with the respective analyte. Finally, we tested the mouse sample material requirements for plasma, bile, and liver samples and determined BA concentrations in C57/BL6N wild-type mice. In conclusion, the LC-MS/MS method presented here permits a rapid and reproducible quantification of the major murine BAs.

Keywords:  Bile; Bile acid; LC–MS/MS; Lipidomics; Liver; Plasma

DOI:  https://doi.org/10.1007/s00216-024-05668-0
Talanta. 2024 Nov 28. pii: S0039-9140(24)01680-1. [Epub ahead of print]285 127298

Integration of feature-based molecular networking and high-definition data-dependent acquisition for the comprehensive multicomponent characterization of Honghua Xiaoyao Tablet.

Siyi Ma, Yuhao Zhang, Renwen Zhu, Shiyu Wu, Shiyu Zhang, Huawu Zeng, Weidong Zhang, Ji Ye.

  Systematically identifying the chemical constituents in complex matrices is a challenge due to the inherent characteristics of compounds. The combination of liquid chromatography-tandem mass spectrometry (LC-MS) and classical molecular networking (CLMN) is a powerful technology for annotating small molecules. However, the low coverage from inappropriate acquisition modes and the inseparability of isomeric compound nodes still hinders the comprehensive metabolite characterization. A novel strategy that integrated high-definition data-dependent acquisition (HDDDA) from traveling-wave ion mobility mass spectrometry (TWIMS) and feature-based molecular networking (FBMN) was developed to improve chemical component characterization and enhance isomeric component discernment. The data-dependent acquisition (DDA) and HDDDA, were effectively and visually evaluated by CLMN and FBMN via the number of nodes, clustered nodes and clusters. Moreover, the efficiency of the three strategies was validated. The results strongly demonstrated that the HDDDA-FBMN strategy improves MS coverage and offers significant advantages for isomer identification. With the assistance of the UNIFI platform, the developed strategy was successfully applied to systematically investigate the chemical profile of Honghua Xiaoyao Tablet (HHXYT), a traditional folk empirical prescription for treating various gynecological diseases. 184 compounds were unambiguously identified or tentatively characterized, including 12 pairs of isomers, and two unreported compounds. In conclusion, this hybrid approach achieves dimensionally enhanced MS data acquisition and visual recognition of isomeric compounds, accelerating the structural characterization in complex systems. We anticipate that HDDDA-FBMN strategies will be a flexible and versatile tool for the chemical components in a complex system of TCMs.

Keywords:  Collision cross section; Feature-based molecular networking; High-definition data-dependent acquisition; Honghua Xiaoyao tablet; Liquid chromatography-tandem mass spectrometry

DOI:  https://doi.org/10.1016/j.talanta.2024.127298
Nat Prod Rep. 2024 Dec 02.

Effective data visualization strategies in untargeted metabolomics.

Kevin Mildau, Henry Ehlers, Mara Meisenburg, Elena Del Pup, Robert A Koetsier, Laura Rosina Torres Ortega, Niek F de Jonge, Kumar Saurabh Singh, Dora Ferreira, Kgalaletso Othibeng, Fidele Tugizimana, Florian Huber, Justin J J van der Hooft.

Covering: 2014 to 2023 for metabolomics, 2002 to 2023 for information visualizationLC-MS/MS-based untargeted metabolomics is a rapidly developing research field spawning increasing numbers of computational metabolomics tools assisting researchers with their complex data processing, analysis, and interpretation tasks. In this article, we review the entire untargeted metabolomics workflow from the perspective of information visualization, visual analytics and visual data integration. Data visualization is a crucial step at every stage of the metabolomics workflow, where it provides core components of data inspection, evaluation, and sharing capabilities. However, due to the large number of available data analysis tools and corresponding visualization components, it is hard for both users and developers to get an overview of what is already available and which tools are suitable for their analysis. In addition, there is little cross-pollination between the fields of data visualization and metabolomics, leaving visual tools to be designed in a secondary and mostly ad hoc fashion. With this review, we aim to bridge the gap between the fields of untargeted metabolomics and data visualization. First, we introduce data visualization to the untargeted metabolomics field as a topic worthy of its own dedicated research, and provide a primer on cutting-edge visualization research into data visualization for both researchers as well as developers active in metabolomics. We extend this primer with a discussion of best practices for data visualization as they have emerged from data visualization studies. Second, we provide a practical roadmap to the visual tool landscape and its use within the untargeted metabolomics field. Here, for several computational analysis stages within the untargeted metabolomics workflow, we provide an overview of commonly used visual strategies with practical examples. In this context, we will also outline promising areas for further research and development. We end the review with a set of recommendations for developers and users on how to make the best use of visualizations for more effective and transparent communication of results.

DOI: https://doi.org/10.1039/d4np00039k
J Chromatogr A. 2024 Nov 30. pii: S0021-9673(24)00930-0. [Epub ahead of print]1740 465557

Simultaneous analysis of reduced and oxidized forms of multiple biological aminothiols in cells and tissues by double derivatization combined with liquid chromatography‒mass spectrometry.

Mindan Wang, Li Liu, Xialian Cui, Xiuping Chen, Yixin Wei, Wenwen Zhang, Hang Yin, Chenguo Feng, Fang Zhang.

  Biological aminothiols (BATs) typically exist in both reduced and oxidized forms, each exhibiting diverse biological activities. Monitoring the levels and ratios of the two forms is crucial for clinical diagnosis and understanding their roles in biological systems. In this study, we developed a method for simultaneous analysis of both reduced and oxidized BATs using a double derivatization approach combined with liquid chromatography-mass spectrometry (LC-MS). The method employed a sequential derivatization strategy: initially, 2‑bromo-N,N-dimethylacetamide (Br-DMA) reacted with the thiol groups of reduced BATs, followed by derivatization of both reduced and oxidized BATs with stable isotope labeling reagents, [d0]-/[d3]-6,7-dimethoxy-3-methyl isochromenylium tetrafluoroborate ([d0]-/[d3]-DMMIC). The methodology validation showed excellent linearity (R2 > 0.99), accuracy (85.07-119.94 %), precision (intraday: 5.26-18.78 %; interday: 6.52-19.01 %), recovery (70.09-119.27 %), and matrix effect (92.69-126.79 %). Finally, the method was successfully applied to nontargeted BAT screening in lung A549 cells, assessing changes in BAT levels in A549 cells upon treatment with the anticancer compounds triptolide and bufalin, and comparing differences in BAT levels between lung adenocarcinoma and paracarcinoma tissues. The results indicated that the developed method could be a comprehensive practical protocol and serve as a platform for profiling reduced and oxidized BATs in biological samples while meeting various analysis demands.

Keywords:  A549 cells; Biological aminothiols; Double derivatization; LC-MS; Lung adenocarcinoma

DOI:  https://doi.org/10.1016/j.chroma.2024.465557
Nature. 2024 Dec 04.

Dietary fructose enhances tumour growth indirectly via interorgan lipid transfer.

Ronald Fowle-Grider, Joe L Rowles, Isabel Shen, Yahui Wang, Michaela Schwaiger-Haber, Alden J Dunham, Kay Jayachandran, Matthew Inkman, Michael Zahner, Fuad J Naser, Madelyn M Jackstadt, Jonathan L Spalding, Sarah Chiang, Kyle S McCommis, Roland E Dolle, Eva T Kramer, Sarah M Zimmerman, George P Souroullas, Brian N Finck, Leah P Shriver, Charles K Kaufman, Julie K Schwarz, Jin Zhang, Gary J Patti.

Fructose consumption has increased considerably over the past five decades, largely due to the widespread use of high-fructose corn syrup as a sweetener1. It has been proposed that fructose promotes the growth of some tumours directly by serving as a fuel2,3. Here we show that fructose supplementation enhances tumour growth in animal models of melanoma, breast cancer and cervical cancer without causing weight gain or insulin resistance. The cancer cells themselves were unable to use fructose readily as a nutrient because they did not express ketohexokinase-C (KHK-C). Primary hepatocytes did express KHK-C, resulting in fructolysis and the excretion of a variety of lipid species, including lysophosphatidylcholines (LPCs). In co-culture experiments, hepatocyte-derived LPCs were consumed by cancer cells and used to generate phosphatidylcholines, the major phospholipid of cell membranes. In vivo, supplementation with high-fructose corn syrup increased several LPC species by more than sevenfold in the serum. Administration of LPCs to mice was sufficient to increase tumour growth. Pharmacological inhibition of ketohexokinase had no direct effect on cancer cells, but it decreased circulating LPC levels and prevented fructose-mediated tumour growth in vivo. These findings reveal that fructose supplementation increases circulating nutrients such as LPCs, which can enhance tumour growth through a cell non-autonomous mechanism.

DOI: https://doi.org/10.1038/s41586-024-08258-3