ArticleJournal of the American Society for Mass Spectrometry2018
Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions.
Article in Journal of the American Society for Mass Spectrometry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- A First-Trimester Serum Proteomic Signature for Early Prediction of Preeclampsia: Integrated Untargeted and Targeted Mass Spectrometry with Machine Learning.Life (Basel, Switzerland) · 2026Article
- Insights into complementary exposomic targeted analysis and suspect screening approaches: a case study examining human serum for chemicals with LC-IMS-MS.Environmental science. Advances · 2026Article
- Integrated Clinical and Molecular Profiling of Fetal Growth Disorders in the First Trimester.International journal of molecular sciences · 2026Article
- Machine Learning and Blood-Targeted Proteomics Enable Early Prediction and Etiological Discrimination of Hypertensive Pregnancy Disorders.International journal of molecular sciences · 2026Article
- Tissue and extracellular matrix remodeling of the subchondral bone during osteoarthritis of knee joints as revealed by spatial mass spectrometry imaging.Bone research · 2026Article
- Plasma Protein Panel for Assessing the Risk of Alzheimer's Disease by MRM-MS Analysis: The Study of Two Independent Clinical Cohorts.International journal of molecular sciences · 2025Article
- Assessment of Variable Traveling Wave Profiles for Small-Molecule Applications in Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS).Journal of the American Society for Mass Spectrometry · 2025Article
- Multiplexed Quantification of First-Trimester Serum Biomarkers in Healthy Pregnancy.International journal of molecular sciences · 2025Article
- Analysis of FAIMS for the study of affinity-purified protein complexes using the orbitrap ascend tribrid mass spectrometer.Molecular omics · 2025Article
- Screening of Protein Carbonylation Sites in Human Serum by Ion Mobility Mass Spectrometry.Journal of proteome research · 2025Article
- Evaluating Ion Mobility Data Acquisition, Calibration, and Processing for Small Molecules: A Cross-Platform Assessment of Drift Tube and Traveling Wave Methodologies.Journal of the American Society for Mass Spectrometry · 2025Article
- Absolute Quantitative Targeted Monitoring of Potential Plasma Protein Biomarkers: A Pilot Study on Healthy Individuals.Biomedicines · 2024Article
- Evaluating Solid Phase Adsorption Toxin Tracking (SPATT) for passive monitoring of per- and polyfluoroalkyl substances (PFAS) with Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS).The Science of the total environment · 2024Article
- First-Trimester Preeclampsia-Induced Disturbance in Maternal Blood Serum Proteome: A Pilot Study.International journal of molecular sciences · 2024Article
- Elucidating the role of lipid interactions in stabilizing the membrane protein KcsA.Biophysical journal · 2024Article
- Mapping microhabitats of lignocellulose decomposition by a microbial consortium.Nature chemical biology · 2024Article
- Computational tools and algorithms for ion mobility spectrometry-mass spectrometry.Proteomics · 2024Review
- Oxidation of chlortetracycline and its isomers by Botrytis aclada laccase in the absence of mediators: pH dependence and identification of transformation products by LC-MS.Biodegradation · 2024Article
- Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids.Nature communications · 2024Article
- METLIN-CCS: an ion mobility spectrometry collision cross section database.Nature methods · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Recent advances in ion mobility spectrometry (IMS) have illustrated its power in determining the structural characteristics of a molecule, especially when coupled with other separations dimensions such as liquid chromatography (LC) and mass spectrometry (MS). However, these three separation techniques together greatly complicate data analyses, making better informatics tools essential for assessing the resulting data. In this manuscript, Skyline was adapted to analyze LC-IMS-CID-MS data from numerous instrument vendor datasets and determine the effect of adding the IMS dimension into the normal LC-MS molecular pipeline. For the initial evaluation, a tryptic digest of bovine serum albumin (BSA) was spiked into a yeast protein digest at seven different concentrations, and Skyline was able to rapidly analyze the MS and CID-MS data for 38 of the BSA peptides. Calibration curves for the precursor and fragment ions were assessed with and without the IMS dimension. In all cases, addition of the IMS dimension removed noise from co-eluting peptides with close m/z values, resulting in calibration curves with greater linearity and lower detection limits. This study presents an important informatics development since to date LC-IMS-CID-MS data from the different instrument vendors is often assessed manually and cannot be analyzed quickly. Because these evaluations require days for the analysis of only a few target molecules in a limited number of samples, it is unfeasible to evaluate hundreds of targets in numerous samples. Thus, this study showcases Skyline's ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly. Graphical Abstract ᅟ.
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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.