Get hands-on experience creating a Skyline document to measure quantitative differences in peptide expression using the MS1 scans from your data dependent acquisition (DDA) experiments. In this tutorial, you will generate a spectral library from a discovery data set, set up a Skyline document for MS1 filtering, import raw mass spectrometer data to extract precursor ion chromatograms from MS1 scans, with peak picking guided by MS/MS peptide identifications, and further process the resulting quantitative data in Skyline. If you are interested in label-free quantitative analysis of discovery data sets, this tutorial will give you a new tool set for your investigation. (38 pages)

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* - written on v1.2, updated for v1.4, revised for v2.5

Also, see our paper in Molecular Cellular Proteomics (please cite)
Platform independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline. Application to protein acetylation and phosphorylation
[abstract]

On October 21st, 2014, the Skyline Team produced Webinar #1: Getting the Most Out of DDA Data with Skyline, another great resource for working with DDA data in Skyline.
[webinar 1]
For an in-depth discussion peptide modifications, see Webinar #10: Working with Modifications in Skyline which was produced on September 29, 2016 by the Skyline Team and features importing PTMs, isotope labeling and importing large assay libraries, among other topics.
[webinar 10]

If you run into trouble seeing ID annotations in your chromatograms, be sure to consult Tip: ID Annotations Missing with Mascot Search Results. Even if you did not use Mascot, this tip may contain useful information.
[tip]


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