Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions

Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline

(2018) Vagisha Sharma et al.   MOLECULAR & CELLULAR PROTEOMICS

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry

(2016) Kristin E. Burnum-Johnson et al.   MOLECULAR & CELLULAR PROTEOMICS

A multicenter study benchmarks software tools for label-free proteome quantification

(2016) Pedro Navarro et al.   NATURE BIOTECHNOLOGY

Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics

(2016) Ute Distler et al.   Nature Protocols

Development of a new ion mobility time-of-flight mass spectrometer

(2015) Yehia M. Ibrahim et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments

(2015) Matthew J. Rardin et al.   MOLECULAR & CELLULAR PROTEOMICS

DIA mass spectrometry

(2015) Allison Doerr   NATURE METHODS

Enhancing bottom-up and top-down proteomic measurements with ion mobility separations

(2015) Erin Shammel Baker et al.   PROTEOMICS

Conformational Ordering of Biomolecules in the Gas Phase: Nitrogen Collision Cross Sections Measured on a Prototype High Resolution Drift Tube Ion Mobility-Mass Spectrometer

(2014) Jody C. May et al.   ANALYTICAL CHEMISTRY

Qualitative and Quantitative Characterization of Plasma Proteins When Incorporating Traveling Wave Ion Mobility into a Liquid Chromatography–Mass Spectrometry Workflow for Biomarker Discovery: Use of Product Ion Quantitation As an Alternative Data Analysis Tool for Label Free Quantitation

(2014) Charlotte E. Daly et al.   ANALYTICAL CHEMISTRY

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets

(2013) Kevin L. Crowell et al.   BIOINFORMATICS

Increasing confidence of LC–MS identifications by utilizing ion mobility spectrometry

(2013) Kevin L. Crowell et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Effects of Traveling Wave Ion Mobility Separation on Data Independent Acquisition in Proteomics Studies

(2013) Pavel V. Shliaha et al.   JOURNAL OF PROTEOME RESEARCH

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

(2013) Ute Distler et al.   NATURE METHODS

Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples

(2012) Scott J. Geromanos et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline

(2012) Birgit Schilling et al.   MOLECULAR & CELLULAR PROTEOMICS

Extracted fragment ion mobility distributions: A new method for complex mixture analysis

(2011) Sunyoung Lee et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Developing IMS–IMS–MS for rapid characterization of abundant proteins in human plasma

(2009) Stephen J. Valentine et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies

(2007) Erin Shammel Baker et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY