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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Exploring Ion Mobility Mass Spectrometry Data File Conversions to Leverage Existing Tools and Enable New Workflows

Ion mobility (IM) is often combined with LC-MS experiments to provide an additional dimension of separation for complex sample analysis. While highly complex samples are better characterized by the full dimensionality of LC-IM-MS experiments to uncover new information, downstream data analysis workflows are often not equipped to properly mine the additional IM dimension. For many samples the data acquisition benefits of including IM separations are all that is necessary to uncover sample information and the full dimensionality of the data is not required for data analysis. Post-acquisition reduction and adaptation of the dimensions of LC-IM-MS and IM-MS experiments into an LC-MS format opens the possibility to use a plethora of existing software tools. In this work, we developed data file conversion tools to reduce the complexity of IM data analysis. Three data file transformations are introduced in the PNNL PreProcessor software: 1) mapping the IM axis to the LC axis for IM-MS data, 2) converting the drift time vs. m/z space to CCS/z vs m/z space, and 3) transforming All Ions IM/MS mobility aligned fragmentation data to a standard LC-MS DDA data file format. Finally, these new data file conversions are demonstrated with corresponding lipidomics and proteomics workflows that leverage existing LC-MS data analysis software to highlight the benefits of the data transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution

The placenta is a complex and heterogeneous organ that links the mother and fetus, playing a crucial role in nourishing and protecting the fetus throughout pregnancy. Integrative spatial multi-omics approaches can provide a systems-level understanding of molecular changes underlying the mechanisms leading to the histological variations of the placenta during healthy pregnancy and pregnancy complications. Herein, we advance our metabolome-informed proteome imaging (MIPI) workflow to include lipidomic imaging, while also expanding the molecular coverage of metabolomic imaging by incorporating on-tissue chemical derivatization (OTCD). The improved MIPI workflow advances biomedical investigations by leveraging state-of-the-art molecular imaging technologies. Lipidome imaging identifies molecular differences between two morphologically distinct compartments of a placental villous functional unit, syncytiotrophoblast (STB) and villous core. Next, our advanced metabolome imaging maps villous functional units with enriched metabolomic activities related to steroid and lipid metabolism, outlining distinct molecular distributions across morphologically different villous compartments. Complementary proteome imaging on these villous functional units reveals a plethora of fatty acid- and steroid-related enzymes uniquely distributed in STB and villous core compartments. Integration across our advanced MIPI imaging modalities enables the reconstruction of active biological pathways of molecular synthesis and maternal-fetal signaling across morphologically distinct placental villous compartments with micrometer-scale resolution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Author Correction: A universal language for finding mass spectrometry data patterns

Correction to: Nature Methodshttps://doi.org/10.1038/s41592-025-02660-z, published online 12 May 2025. This article was originally published under standard Springer Nature license (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license, © The Author(s). The error has been corrected in the HTML and PDF versions of the article.

Damiani, Tito↗
DOE OSTI2023

Detection and confirmation of fentanyls in high clay‐content soil by electron ionization gas chromatography‐mass spectrometry

Abstract Detection of illicit drugs in the environment, particularly in soils, often suggests the present or past location of a clandestine production center for these substances. Thus, development of efficient methods for the analysis and detection of these chemicals is of paramount importance in the field of chemical forensics. In this work, a method involving the extraction and retrospective confirmation of fentanyl, acetylfentanyl, thiofentanyl, and acetylthiofentanyl using trichloroethoxycarbonylation chemistry in a high clay‐content soil is presented. The soil was spiked separately with each fentanyl at two concentrations (1 and 10 μg/g) and their extraction accomplished using ethyl acetate and aqueous NH 4 OH (pH ~ 11.4) with extraction recoveries ranging from ~56% to 82% for the high‐concentration (10 μg/g) samples while ranging from ~68% to 83% for the low‐concentration (1 μg/g) samples. After their extraction, residues containing each fentanyl were reacted with 2,2,2‐trichloroethoxycarbonyl chloride (Troc‐Cl) to generate two unique and predictable products from each opioid that can be used to retrospectively confirm their presence and identity using EI‐GC‐MS. The method's limit of detection (MDL/LOD) for Troc‐norfentanyl and Troc‐noracetylfentanyl were estimated to be 29.4 and 31.8 ng/mL in the organic extracts. In addition, the method's limit of quantitation for Troc‐norfentanyl and Troc‐noracetylfentanyl were determined to be 88.2 and 95.5 ng/mL, respectively. Collectively, the results presented herein strengthen the use of chloroformate chemistry as an additional chemical tool to confirm the presence of these highly toxic and lethal substances in the environment.

Valdez, Carlos A.↗
DOE OSTI2023

Mass Spectrometry–Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine

Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.

60 APPLIED LIFE SCIENCES↗