Familiarization guide overview - Proteome Discoverer Software - Familiarization guide overview - Proteome Discoverer Software - Proteome Discoverer Software

This guide provides six tutorial exercises that help new users learn to use the Proteome Discoverer 3.1 application. All raw data files can be found either in the Proteome Discoverer 3.1 medium folder located on the provided USB or from the Proteome Discoverer 3.1 folder on the software download and licensing portal (https://thermo.flexnetoperations.com/). Each chapter contains one tutorial that is complete and independent of the others. That is, the chapters do not need to be completed in sequence.

• Chapter 1, “Analysis of yeast gene knockouts by multiplexed reporter ion quantification.”
• Chapter 2, “Reporter ion quantification with phosphorylation.”
• Chapter 3, “Label-free quantitation with spiked-in proteins.”
• Chapter 4, “SILAC 3plex of E. coli proteins mixed with known ratios.”
• Chapter 5, “Analysis of yeast gene knockouts by multiplexed reporter ion quantification with two replicates.”
• Chapter 6, "Data independent analysis of proteome mixtures using CHIMERYS"

However, each tutorial touches on different aspects of the application. In particular, new users will find it easier to start with Chapter 1, which describes using one replicate before starting the tutorial in Chapter 5, describes using two. Also, the more tutorials you complete, the broader your application knowledge. The following table lists the aspects of each tutorial.