ArticleJournal of proteome research2020
Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics.
Article in Journal of proteome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 329 papers.
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Who cites it
329 citing papers in PubMed.
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- Very Long Chain Fatty Acid Synthesis is a Targetable Dependency in RAS Pathway Mutant Leukemia.Blood cancer discovery · 2026Article
- TET2 loss triggers ssDNA gap accumulation and heightened PARP inhibitor sensitivity.Nature communications · 2026Article
- Metabolomic correlates of intravenous racemic ketamine in treatment-resistant major depressive disorder: the Bio-K/NNDC multicenter trial.The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry · 2026Article
- Impact of blood contamination on hydrophilic metabolomics in human meningioma tissue.Analytical and bioanalytical chemistry · 2026Article
- Mannose supports lung cancer metabolism during glycolytic limitation.EMBO reports · 2026Article
- Microbiome-associated metabolites, valerobetaine and homocarnitine, inhibit carnitine transport via OCTN2.American journal of physiology. Cell physiology · 2026Article
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- Effect of Late Second to Early Third Trimester of Pregnancy on the Activity of Renal Organic Anion Transporters (OAT1 and OAT3): A Biomarker Study.Clinical pharmacology and therapeutics · 2026Article
- S1P receptor 1 signaling reduces arterial thrombosis via up-regulation of endothelial thrombomodulin expression.Science advances · 2026Article
- Sustained loss ofbioRxiv : the preprint server for biology · 2026Article
- Persistent and Mobile Organic Contaminants: Quantification and Nontarget Analysis in Greater Boston Drinking and Surface Water.ACS environmental Au · 2026Article
- KRAS Signaling Inhibition Induces a Targetable Metabolic Dependency on Lipophagy-Dependent Fatty Acid Oxidation in Pancreatic Cancer.Cancer research · 2026Article
269 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source software tool for targeted quantitative mass spectrometry method development and data processing with a 10 year history supporting six major instrument vendors. Designed initially for proteomics analysis, we describe the expansion of Skyline to data for small molecule analysis, including selected reaction monitoring, high-resolution mass spectrometry, and calibrated quantification. This fundamental expansion of Skyline from a peptide-sequence-centric tool to a molecule-centric tool makes it agnostic to the source of the molecule while retaining Skyline features critical for workflows in both peptide and more general biomolecular research. The data visualization and interrogation features already available in Skyline, such as peak picking, chromatographic alignment, and transition selection, have been adapted to support small molecule data, including metabolomics. Herein, we explain the conceptual workflow for small molecule analysis using Skyline, demonstrate Skyline performance benchmarked against a comparable instrument vendor software tool, and present additional real-world applications. Further, we include step-by-step instructions on using Skyline for small molecule quantitative method development and data analysis on data acquired with a variety of mass spectrometers from multiple instrument vendors.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.