Webinar - An introduction to ProteoIQ 1.5 by oxu11283

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									INTRODUCTION TO PROTEOIQ
       VERSION 1.5
                WHAT’S NEW


Performance Optimization

Vastly improved Quantitation Tools and Settings

New Visualization Tools

Introduction of support for Concatenated Database
searches making the number of statistical validation
methods available within the software to over ten!
QUANTITATION SETTING IMPROVEMENTS –
           REPORTER IONS

 Modify reporter ion selection mass window after
 project creation
      Works both with new and old ProteoIQ projects
      Create multiple protein sets with various reporter
      ion selection mass windows

      Easily verify what data you trust for each instrument
      in your lab

      Modify reference group (denominator, 117/114)

      ProteoIQ reports the number of peptides containing
      “detected” reporter ions
EDIT>MODIFY REPORTER
QUANT SETTINGS
QUANTITATION SETTING IMPROVEMENTS –
             LABEL-FREE


 Change reference group
   Default quantitation mode is to have the global average
   as the reference group. Version 1.5 – change reference
   group

   Set one or more groups as your internal control

   Create multiple sets with different reference groups and
   easily observe how it affects your data
EDIT>LABEL FREE QUANT
SETTINGS
PEPTIDE LEVEL REPORTER ION QUANTITATION
  AND ENHANCED PEPTIDE VISUALIZATION


 Display Log2 Relative Expression for each peptide



 Visualize protein sequence coverage based on
 selected peptides



 For reporter ion quantitation this allows the detection
 of truncated products or isoforms (discordant
 peptide expression ratios)
PEPTIDE REPORTER ION LOG2 EXPRESSION

                    Log2 Relative Expression for 
                           each peptide




                      Select View>Peptide Table 
                       Options>Select Columns
                        to display Log2 Relative 
                              Expression
VIEW SEQUENCE COVERAGE BY SELECTED PEPTIDES




     Right click peptide sequences then 
           select:  Update Protein 
     Sequence>Show Selected Peptides
  GROUP SUMMARY - VENN DIAGRAM


Provides an overview of protein, peptide, or protein
group distributions across selected groups

Freedom to choose the biological groups that are of
interest to you

Select more than one group at a time

Select regions of the Venn Diagram to select
peptides, proteins, or protein groups in the
protein/peptide set viewer

Functions in both Traditional and Strict modes
GROUP SUMMARY - VENN DIAGRAM



    Select groups to display




     Select data 
       source

      Select Venn 
     diagram type
    VENN DIAGRAM – TRADITIONAL MODE

  This information is reported regardless of whether
  they are found in other groups (see example below)
     i.e. Found in A, but may also be in B or C

  No concept of uniqueness

              Biological  Group A Biological Group B   Intersection 
                                                          A and B
# Proteins           10                   10                5




                          10     5         10
VENN DIAGRAM – TRADITIONAL MODE



                              Total protein 
                           groups in patient 2




        Total protein 
     groups in patient 1
        VENN DIAGRAM – STRICT MODE

 Each area represents strictly defined data set
    i.e. Only in A, but not in B or C, etc.

 Eases peptide level quantitation greatly
    Now with one click you can ID all peptides that are
    common or unique between groups

              Biological  Group A Biological Group B   Intersection
                                                          A and B
# Proteins           10                   10                5




                          5      5         5
VENN DIAGRAM – STRICT MODE



                               Total “UNIQUE” 
                              protein groups in 
                                  patient 2




   “Common” protein groups 
    between patient 1 and 2
  FALSE DISCOVERY RATE (FDR) VIA
CONCATENATED DATABASE SEARCHING

Previous version of ProteoIQ supported FDR via
separate searches of target and decoy databases (a
more conservative approach)

ProteoIQ can now perform FDR calculations for
searches generated with concatenated target and
decoy databases (greater sensitivity but less
stringency)

Cuts necessary search time in half

Recent publications have noted the importance of
protein false discovery rate analysis
  Reiter et al., Protein identification false discovery rates for very large
  proteomics data sets generated by tandem mass spectrometry. Mol. Cell.
  Proteomics, 2009, 8, 2405-17
PROTEOIQ IS THE ONLY SOFTWARE THAT PROVIDES
 TEN METHODS FOR STATISTICAL VALIDATION OF
            PROTEOMIC DATA SETS
  Score Filtering           T/D Discriminant Score
                            FDR
  Peptide Probability
                            Concatenated Peptide
  Protein Probability       FDR
  Protein Group             Concatenated Protein
  Probability               FDR
  T/D Peptide FDR           Concatenated
  T/D Protein FDR           Disciminant Score FDR

  Note: No single statistical validation method is
  appropriate for all experimental designs!
 HOW TO IMPORT A CONCATENATED DB


Only two new requirements have been added to the
Modify Database Wizard

Concatenated DB must be specified in the Database
Type drop down menu

When inputting your parse rule, ProteoIQ will ask for
a decoy identifier
  This simply tells ProteoIQ which entries in your DB are
  decoys
  Example: RANDOM, r-, REV, etc

Note: As always, if you need any help determining
what your decoy identifier is, we can surely help.
CONCATENATED T/D DB – MODIFY
     DATABASE WIZARD

                 Select “Concatenated Target + 
                        Decoy” DB Type
    CREATING A CONCATENATED TARGET AND
       DECOY DATABASE FOR PROTEOIQ




Note: a UNIQUE identifier must be added to the decoy database

Note: The parse rule for the target DB must also function for the
decoy database
CONCATENATED T/D DB – ADDING THE
     DECOY IDENTIFIER RULE




 Enter the decoy identifier. 
  Note: this must be in ().
 THANK YOU FOR ATTENDING AND DON’T
FORGET THE UPCOMING WEBINAR SERIES!


Getting to the right answers - a non-statisticians guide
to validating protein identifications (January 26, 2pm
EST)

Who needs isotopic labels - a practical guide to label
free quantitation by spectral counting (February 16,
2pm EST)

Getting better results out of your $1000 reagents – a
step-by-step guide to isobaric tag quantification in
ProteoIQ (February 23, 2pm EST)
             CONTACT INFORMATION


BioInquire

220 Riverbend Rd, Suite 103

Athens GA, 30602

Office: 706-583-4000

Email: support@bioinquire.com

      sales@bioinquire.com

For more information: www.bioinquire.com

								
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