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─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics.
J Proteome Res
January 2025
Functional Genomics Center Zurich (FGCZ) - University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis () of proteins. As experiments grow in complexity, involving more samples, groups, and identified proteins, interactive differential expression analysis tools become impractical. The addresses this challenge by providing a command-line interface that simplifies , making it accessible to nonprogrammers and seamlessly integrating it into workflow management systems.
View Article and Find Full Text PDFThe relevance of endoplasmic reticulum lumen and Anoctamin-8 for major depression: Results from a systems biology study.
J Psychiatr Res
January 2025
Laboratory of Molecular Psychiatry. Rua Ramiro Barcelos, Centro de Pesquisa Experimental - Hospital de Clínicas de Porto Alegre (HCPA), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 2350, Brazil; Postgraduate Program of Psychiatry and Behavioral Sciences. Rua Ramiro Barcelos, Department of Psychiatry, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, 2400, Brazil.
Major depressive disorder (MDD) is a highly prevalent and debilitating disorder, yet its pathophysiology has not been fully elucidated. The aim of this study is to identify novel potential proteins and biological processes associated with MDD through a systems biology approach. Original articles involving the measurement of proteins in the blood of patients diagnosed with MDD were selected.
View Article and Find Full Text PDFMass Spectrometry-Based Spatial Multiomics Revealed Bioaccumulation Preference and Region-Specific Responses of PFOS in Mice Cardiac Tissue.
Environ Sci Technol
January 2025
State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, 999077, China.
The distribution and bioaccumulation of environmental pollutants are essential to understanding their toxicological mechanism. However, achieving spatial resolution at the subtissue level is still challenging. Perfluorooctanesulfonate (PFOS) is a persistent environmental pollutant with widespread occurrence.
View Article and Find Full Text PDFGlobal cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.
Sci Adv
January 2025
Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multiomic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in and mutants, where lysosomes accumulate cholesterol.
View Article and Find Full Text PDFStudies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as "omics") data allow researchers to find biomarkers or molecular targets or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data are multidimensional, and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries do not allow exploration of detailed patterns in omics data that may have biological relevance.
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