Get hands-on experience working with targeted MS/MS (also referred to as parallel reaction monitoring - PRM) data acquired on a low resolution Thermo LTQ and a high resolution Agilent 6520 Q-TOF. Gain new understanding of the selectivity and sensitivity differences between peptide quantification using precursor and fragment ions measured on low and high resolution instruments. Discover new ways to work with and understand your own mass spectrometry data using the rich feature set provided by Skyline for working with chromatography-based quantitative proteomics. (40 pages)
* - written on v1.2, updated for v1.4, revised for v2.5
Also, see our paper in Journal of Proteome Research (please cite)
Label-Free Quantitation of Protein Modifications by Pseudo-Selected Reaction Monitoring with Internal Reference Peptides
On January 13th, 2015, the Skyline Team produced Webinar #3: PRM Targeted Proteomics Using Full-Scan MS and Skyline, another great resource for producing and working with PRM data in Skyline.
On July 21, 2015, the Skyline Team produced Webinar #9: PRM for PTM Studies more advanced discussion that covered using PRM data from a study of modifications on histones.
On January 16, 2018, the Skyline Team produced Webinar #13: PRM Method Development and Data Analysis a more complete and modern PRM tutorial using Thermo Fusion data.