1. ProteinPilot ™ Software © 2008 Applera Corporation and MDS Inc.

2. ProteinPilot ™ Software © 2008 Applera Corporation and MDS Inc. Identify more proteins with greater sequence coverage Lightening-fast Peptidomics: no-enzyme digests without increasing false positives Quantify isoforms separately AB SCIEX Protein Research Solutions for Global Discovery Proteomics

3. ProteinPilot ™ Software © 2008 Applera Corporation and MDS Inc. This takes you from raw data to complete protein and peptide ID and quantitation in a single click followed by robust protein assembly with the ProGroup ™ Algorithm. Quantitative analysis can be included for samples labeled with iTRAQ ® Reagents – 8plex or you can send it to the next generation Paragon ™ Algorithm for peptide ID… You can send searches to the industry standard Mascot ® search engine… ProteinPilot ™ Software gives you a full ‘pipeline’ in a single tool… One touch productivity. Complete Peptide/Protein ID & Quant Raw mass spec data MASCOT ID results Paragon ™ Algorithm Pro Group ™ Algorithm Quantitation analysis Peak list creation, quant areas MASCOT ® search engine AB SCIEX Protein Research Solutions for Global Discovery Proteomics

4. ProteinPilot ™ Software © 2008 Applera Corporation and MDS Inc. The combination of these two innovations allows the Paragon ™ Algorithm to identify peptides that conventional search engines can not. The same idea is applied to digestion features, tolerances, etc. 1. A new kind of sequence tag algorithm. 2. The description of modifications using probability Mol. Cell. Proteomics, 6:1638-1655, (2007) The Paragon™ Algorithm uses two key innovations to dramatically improve what portion of your acquired spectra you can identify. 1. A new kind of sequence tag algorithm. It understands the relevance of each area of the database on a grayscale using a measure called Sequence Temperature Value (STV) 2. The description of modifications using probability instead of the conventional rules that allow or forbid features. AB SCIEX Protein Research Solutions for Global Discovery Proteomics

5. ProteinPilot ™ Software © 2008 Applera Corporation and MDS Inc. In this independent study from the University of Michigan, the Paragon ™ Algorithm identifies the largest number of spectra But good peptide identification is not enough… Slides courtesy P. Jagtap and P. Andrews, University of Michigan MascotParagonSequestX !Tandem 3964 576 2060 Bdellovibrio dataset (1% FPR) Spectra IDs First dataset 0 15000 10000 5000 1301013360 11803 14955 X! TandemMascotSequestParagon Spectra IDs X! TandemMascotSequestParagon 4385 3958 4540 6024 Spectra IDs Human dataset (1% FPR) Second dataset X! TandemMascotSequestParagon 8397 8743 8002 9259 10000 7500 5000 2500 0 7500 4500 2500 0 6000 1500 AB SCIEX Protein Research Solutions for Global Discovery Proteomics

6. ProteinPilot ™ Software © 2008 Applera Corporation and MDS Inc. The minimal solution. Only protein A is detected here with high confidence. There is a hint of a second protein, but not with reasonable confidence. The Pro Group ™ Algorithm gives you one of the most defensible protein lists in proteomics without any further steps. A B C (very weak peptide ID) AB SCIEX Protein Research Solutions for Global Discovery Proteomics

7. ProteinPilot ™ Software © 2008 Applera Corporation and MDS Inc. Despite all of these advances in results quality, ProteinPilot ™ Software is amazingly easy to use… Just describe the sample, what you want to know, and the effort to invest. And all the ‘algorithmic’ knobs of conventional search engines are gone. You do not need any informatics or mass spec. expertise to get top quality results… One touch productivity. AB SCIEX Protein Research Solutions for Global Discovery Proteomics