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Getting lists of data out of Skyline

Skyline Lists

Skyline

Skyline Lists

Skyline 19.1 added new feature "Lists" which allows you to add arbitrary lists of data to a Skyline document.

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	Attached Files

SkylineLists.pptx

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Skyline Targeted Mass Spec Environment

Install 64-bit Skyline 23.1

	Install 64-bit Skyline 23.1 Unplugged
	Skyline 23.1 Administrator Install

Install 32-bit Skyline (deprecated)

Install 32-bit Skyline Unplugged

教程 (中国语文)

	靶向方法编辑
	靶向方法优化
	分析分类研究的数据
	处理已有定量实验数据
	MS1 全扫描筛选
	针对 MS1 筛选的 DDA 搜索
	并行反应监测 (PRM)
	非数据依赖型采集
	SWATH 数据分析
	小分子目标
	小分子方法开发与 CE 优化
	小分子定量
	绝对定量
	自定义实时报告
	iRT 保留时间预测

チュートリアル（日本語版）

	ターゲットメソッドの編集
	ターゲットメソッドの最適化
	によるグループ研究データの処理
	既存データ処理および定量実験
	MS1フルスキャンフィルタ
	MS1 フィルタ用 DDA 検索
	併発反応モニタリング（PRM）
	DIA、データ非依存性解析
	SWATHデータの分析
	によるターゲットメタボロミクス解析
	小分子メソッド開発とCE最適化
	小分子の定量化
	絶対定量
	カスタムレポートとライブレポート
	iRT保持時間予測

Targeted Method Editing

Targeted Method Refinement

Processing Grouped Study Data

Existing and Quantitative Experiments

MS1 Full-Scan Filtering

DDA Search for MS1 Filtering

Parallel Reaction Monitoring (PRM)

Basic Data Independent Acquisition

Analysis of DIA/SWATH Data

Analysis of diaPASEF Data

Small Molecule Targets

Small Molecule Method Development and CE Optimization

Small Molecule Multidimensional Spectral Libraries

Small Molecule Quantification

Hi-Res Metabolomics

Absolute Quantification

Advanced Peak Picking Models

iRT Retention Time Prediction

Collision Energy Optimization

Ion Mobility Spectrum Filtering

Spectral Library Explorer

QuaSAR Quantitative Statistics

ETH Targeted Proteomics Course Tutorials

	Video 1: Method Editing
	Video 2: Results Analysis
	Video 3: Existing & Quantitative Experiments
	Video: Trailer

YouTube Channels

Terminology Cheat Sheet

Installing Skyline

	Recovering From a Broken Installation
	Recovering the .sky File Extension Association
	Running Skyline TeamCity Artifact Builds

Small Molecules

	Automatic Precursor Isotopes
	UI Modes
	Adduct Descriptions and Small Molecule Labels

Getting lists of data out of Skyline

	Pivot Editor
	Document Grid Number and Date Formats
	Skyline Lists
	Result File Rules in Skyline 20.2
	Hierarchical Clustering (and PCA Plots) in Skyline-daily

DIA (Data Independent Acquisition)

	Generating an Overlapping Window Isolation List using Skyline
	Full Spectrum Demultiplexing of Overlapped DIA Windows using MSConvert
	Import OpenSWATH Results
	Slides Explaining Data Independent Acquisition
	DIA Methods for Thermo Q Exactive

	Normalization Methods
	Batch Calibration
	SureQuant and Triggered Acquisition
	Surrogate Standards
	How Skyline Calculates Peak Areas and Heights

Skyline System Requirements

Parallel Import Performance

Vendor-Specific Instrument Tuning Parameters

	Support for Bruker TOF Instruments
	SCIEX Instrument Settings
	Export SRM Methods for a Thermo LTQ

Integration with Other Tools

	How Skyline Builds Spectral Libraries
	ID Annotations Missing with Mascot Search Results

Share Skyline Documents in Manuscripts

Sharing MS/MS Spectra with Manuscripts

	ExD ion types
	Peak Area Dotp Line Plot
	Synchronized Integration
	Skyline and Java
	Skyline Protein Association
	Spectrum Filters in Skyline 23.1
	EncyclopeDIA Search from Skyline 23.1
	Skyline Batch
	Skyline File Types and Extensions
	Waters SONAR Calibration
	Audit Logging
	Crosslinking
	New in Skyline 4.1
	How to Display Multiple Peptides
	Ion Mobility Separation (IMS) Data

Skyline Source Code

How to build Skyline

	ASMS 2012 WOA am MacLean Presentation
	ASMS 2020 WOA am MacLean Presentation

License Agreement

	How You Can Help
	Get Involved
	3rd-Party Software
	Related

Seattle Quant: A Resource for the Skyline Software Ecosystem

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