BioInquire ProteoIQ

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract ProteoIQ by BioInquire, is one of the most advanced software products for comparative and quantitative proteomics. Built for a demanding research environment, ProteoIQ supports the entire proteomic data analysis pipeline, from statistical validation to quantification.

ProteoIQ features/capabilities include:

Custom Grouping --

Describe Your Proteome -

1) Organize your Search Results;

2) Group by Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (MudPIT) or Two-Dimensional Gel Electrophoresis (2D PAGE) or;

3) Choose Custom File Grouping; Unlimited biological groups or replicates.

Describe Your Samples -

1) Assign unique Descriptions for each biological Group;

2) Assign Replicates;

3) All Data keeps their Assigned Names (spectral counts, peptide scores, sequence coverage, et al);

4) Collaborators and Customers can Interpret with Ease.

Grouping Files -

1) Match Database search results with Biological Samples or Replicates;

2) Drag-and-Drop Efficiency;

3) Quick and Easy Sorting;

4) Add Multiple search Results for the same Tandem Mass Spectrometry (MS/MS) file;

5) Monitor Changes in your Separation Scheme.

Statistical Validation --

False Discovery Rates -

1) Estimate global error rates with false discovery rate calculations at the protein and peptide level;

2) Use either separate or merged target and decoy databases;

3) Limit the frequency of random assignments;

4) Generate plots based on Mascot (see G6G Abstract Number 20087) or SEQUEST scores, discriminate scores or probabilities.

Probability -

1) Model distributions of correct versus incorrect assignments;

2) Assess reliability using a visual representation;

3) Save results as images or as text.

Assess Sensitivity and Error -

1) Create an effective balance between sensitivity and allowable error;

2) Maximize the number of protein identifications by choosing how to filter data;

3) Maintain an acceptable error rate.

Comprehensive Data Reporting -

1) Display all scores and metrics associated with every peptide and protein assignment;

2) Track how protein sets are filtered;

3) Customize results views to fit your needs.

Proteome Visualization --

View Proteins and Peptides -

1) No need for endless spreadsheets;

2) User-friendly interface displays every identified protein or peptide;

3) Sort, search and compare differences between samples;

4) Sort results based on over 33 key metrics.

Customizable Results View -

1) Tailor how you view results;

2) Display only data important to your research;

3) Create custom views for each client or collaborator.

Protein Sequence View -

1) Focus on key proteins and peptides;

2) Access detailed information about every protein identification;

3) Reveal protein sequence coverage, peptide modifications and relative expression between biological groups;

4) Hyperlink to important biological databases.

Comparative Proteomics --

Find Differences and Similarities

1) Select protein sets and choose from three comparisons functions;

2) Compare by difference or intersection;

3) Use the “Union” function to merge protein sets.

Label Free Quantification --

Create Scatter Plots -

1) Compare spectral count abundances to one or more biological samples;

2) Monitor reproducibility using dynamic charts;

3) Find truly significant deviations in protein expressions.

Create Heat Maps -

1) Create customizable heat maps;

2) Select which samples to display and the type of metric;

3) Choose formatting for the table;

4) Save heat maps as images;

5) Use results in other software applications.

Refine your search --

Create Subset Databases -

1) Create a FASTA database from your identified proteins;

2) Repeat searches with unlimited Post Translational Modifications (PTMs) or enzyme cleavage rules;

3) Submit FASTA database to Basic Local Alignment Search Tool (BLAST) or Signal peptide prediction and localization (SignalP).

Group Many Search Results From a Single MS/MS File -

1) Combine results from multiple database searches;

2) Expand your proteome coverage by using many modifications or enzyme cleavage rules;

3) For example, a strict tryptic cleavage search and a semi tryptic cleavage search can be combined.

Filter Results by Modification or Enzyme Specificity -

1) Easily filter results using the “Filter Pane”;

2) Choose from specific modifications or cleavage rules used during the search.

Collaborate and Share --

Free ProteoIQ Viewer -

1) Share results easily, No cumbersome spreadsheets needed;

2) Validate protein identifications before sharing with customers;

3) Give clients freedom to compare and manipulate results.

Export Results in Multiple Formats -

1) Export Protein and Peptide Identifications as text files;

2) Use results for further analysis in other programs;

3) Create FASTA file of identified protein sequences;

4) Use to further search or submit to biological databases.

Publish Proteomics Data to the Web -

1) Create dynamic web pages of your proteomics results;

2) Publish protein and peptide identifications to the web;

3) Share data with collaborators remotely.

Database Wizard --

Database Management Made Simple -

1) Automatic error checking provides accurate results;

2) Select your database;

3) Name, assign, and describe on one page;

4) Follow the intuitive, step-by-step Wizard.

Link Protein Identifications to External Biological Databases -

1) Hyperlink to public or local databases;

2) Link protein identifications to GenBank ( is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations), SwissProt (a manually curated biological database of protein sequences), or Gene Data Base (GeneDB);

3) Use the Protein Viewer for easy navigation.

Subtractive Proteomics Enabled -

1) Non-target database search strategy;

2) Compare search results between two (2) different databases;

3) Filter out contaminating spectra;

4) Identify novel protein identifications in RNA or DNA databases.

System Requirements

Contact manufacturer.


Manufacturer Web Site BioInquire ProteoIQ

Price Contact manufacturer.

G6G Abstract Number 20201

G6G Manufacturer Number 100429