Harnessing the proteome: ProteoIQ Quantitative Proteomics Software Webinar

James AtwoodGeneral Manager US

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Our Mission: Our Mission: Empower Proteomic Data Analysis Empower Proteomic Data Analysis

With ProteoIQ With ProteoIQ all your proteomic analysis is centralizedall your proteomic analysis is centralized

Multiple software platforms for each type of proteomic analysis

Now a single software package for all proteomic studies

ProteoIQ is a Better WayProteoIQ is a Better WayCentralized vendor independent software to enable faster and more accurate data analysis

Sample Prep

MSMS/MS Search

QuantCompare Biology

ProteoIQ Provides a Comprehensive Feature SetProteoIQ Provides a Comprehensive Feature Set

Indicates features available in Scaffold Software

Robust Data Integration in ProteoIQRobust Data Integration in ProteoIQ

Robust data integration•Unlimited enzyme and modification support

• Combine multiple search engine and instrument results.

Accurately Model Your Experimental DesignAccurately Model Your Experimental Design

Experimental Design•ProteoIQ provides a unique multi-level file grouping structure

• Quantify protein expression across samples, replicates, or fractions

• Ensures support for all types of proteomic experiments including large scale clinical proteomics and basic protein identification

Value•Advanced normalizations•Error reduction•Improve quant confidence

ProteoIQ Delivers Industry Leading Data VisualizationProteoIQ Delivers Industry Leading Data Visualization

GlobalChange

ProteinCentric

PeptideCentric

MSCentric

ProteoIQ Delivers Unrivaled Data InteractionProteoIQ Delivers Unrivaled Data Interaction

50+ Data Types 2000+ Filter Conditions 20+ Dynamic Plots

Rapid Qualitative Comparisons with ProteoIQRapid Qualitative Comparisons with ProteoIQ

Qualitative Comparisons•Assess global proteome changes or sampling deviations

• Click to select unique proteins or proteins shared between multiple groups

• Perform set logic on selected protein sets

Value•Rapid identification of protein/peptide subsets•Drill down prior to quantification•No more need for excel

Enhanced Spectral Count Quantification in ProteoIQEnhanced Spectral Count Quantification in ProteoIQ

Spectral counting•Compare and normalize expression across replicates and groups

• Remove outliers and analyze reproducivility

• Quickly select up or down regulated proteins

Robust Isobaric Tag Quantification in ProteoIQRobust Isobaric Tag Quantification in ProteoIQ

Support for common workflowsiTRAQ duplexiTRAQ fourplexiTRAQ eightplexTandem Mass Tags (TMT) duplexTandem Mass Tags (TMT) sixplexOr create your own custom reagent

ProteoIQ Supports Isotopic Label Based QuantificationProteoIQ Supports Isotopic Label Based Quantification

Support for common workflowsSILACICATDimethyl labeling18O15NAcetylation

Value•Quantify more peptides by combining multiple search result types•Ensure accuracy through complete quant control•Deploy S/N thresholds, baseline detection and smoothing

Label Free Quantification in ProteoIQLabel Free Quantification in ProteoIQ

Simple workflow1. Define samples, replicates, or fractions2. Enter DB search results and instrument files3. Select customizable label free quant parameters4. ProteoIQ extracts peak intensities for every peptide from your MS files5. Extracted ion chromatograms are generated for every peptide

Anything but black box software

•Dynamic extracted ion chromatograms•Instant access to all MS and MS/MS data•Control every aspect of quant

ProteoIQ Helps You Get to Biology QuickerProteoIQ Helps You Get to Biology Quicker

“Another goal that I think is not quite so near-term but is certainly achievable or, at least, worth the attempt, is to use proteomics to eventually get enough information that we can understand how different biological processes are controlled within the cell and how they interconnect with each other. “ Ruedi Aebersold. Science Watch 2004

Biological Annotation in ProteoIQBiological pathwaysProtein localizationProtein functionMembrane spanning domainsSignal peptide predictionsCross referencing DNA/RNA expression

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