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Home >> Products >> ProteoIQ >> Features Comparison
| Feature | ProteoIQ Base | ProteoIQ Isobaric | ProteoIQ Isotopic | ProteoIQ Label Free | Scaffold | Proteome Discoverer | Sieve |
| Wizards and customizable workflows | Y | Y | Y | Y | Y | Y | N |
| Command line processing | Y | Y | Y | Y | Y | N | N |
| Free data viewer | Y | Y | Y | Y | Y | N | N |
| Combine DB search results | Y | Y | Y | Y | Y | Y | N |
| Mascot results integration | Y | Y | Y | Y | Y | Y | N |
| SEQUEST results integration | Y | Y | Y | Y | Y | Y | Y |
| Proteome Discover results integration | Y | Y | Y | Y | Y | Y | Y |
| Protein Pilot results integration | Y | Y | Y | Y | Y | N | N |
| X!Tandem results integration | Y | Y | Y | Y | Y | N | N |
| PepXML results integration | Y | Y | Y | Y | Y | N | N |
| Combined enzyme rule support | Y | Y | Y | Y | Y | Y | Y |
| MudPit workflows | Y | Y | Y | Y | N | N | N |
| GeLC workflows | Y | Y | Y | Y | N | N | N |
| Peptide FDR-concatenated DB | Y | Y | Y | Y | N | N | N |
| Protein FDR-concatenated DB | Y | Y | Y | Y | N | N | N |
| Peptide FDR-separate target/decoy DB | Y | Y | Y | Y | N | N | N |
| Protein FDR-separate target/decoy DB | Y | Y | Y | Y | N | N | N |
| Peptide probability | Y | Y | Y | Y | Y | Y | N |
| Protein probability | Y | Y | Y | Y | Y | Y | N |
| Protein parsimony analysis | Y | Y | Y | Y | Y | Y | N |
| 60 filters | Y | Y | Y | Y | N | N | N |
| 17 interactive Plots | Y | Y | Y | Y | N | N | N |
| Peptidomic centric view | Y | Y | Y | Y | Y | Y | Y |
| Proteomic centric view | Y | Y | Y | Y | Y | Y | Y |
| Sequence verification view | Y | Y | Y | Y | Y | Y | Y |
| MS/MS spectral views | Y | Y | Y | Y | Y | Y | N |
| Create multiple protein sets | Y | Y | Y | Y | N | N | N |
| Extract proteins/peptides from list | Y | Y | Y | Y | N | N | N |
| Difference Function | Y | Y | Y | Y | N | N | N |
| Intersection Function | Y | Y | Y | Y | N | N | N |
| Union Function | Y | Y | Y | Y | N | N | N |
| Search for neutral losses | Y | Y | Y | Y | N | N | N |
| Query for peptides by PTM | Y | Y | Y | Y | Y | Y | N |
| Extract PTM containing peptides | Y | Y | Y | Y | N | Y | N |
| GO Terms | Y | Y | Y | Y | Y | Y | N |
| KEGG Pathways | Y | Y | Y | Y | N | N | N |
| Display membrane domains | Y | Y | Y | Y | N | N | N |
| Display signal peptides | Y | Y | Y | Y | N | N | N |
| Integrated transcriptomic data | Y | Y | Y | Y | N | N | N |
| Export according to PSI standards | Y | Y | Y | Y | Y | Y | N |
| Export to FASTA | Y | Y | Y | Y | Y | Y | N |
| Export peptides | Y | Y | Y | Y | Y | Y | Y |
| Export proteins | Y | Y | Y | Y | Y | Y | Y |
| Export MS/MS spectra | Y | Y | Y | Y | N | N | N |
| Create web pages for LIMS integration | Y | Y | Y | Y | N | N | N |
| Compare/Quantify across samples | Y | Y | Y | Y | Y | Y | Y |
| Compare/Quantify across replicates | Y | Y | Y | Y | N | N | N |
| Group/Replicate level filtering | Y | Y | Y | Y | N | N | N |
| Qualitative peptide/protein views | Y | Y | Y | Y | Y | Y | Y |
| Spectral count quantification (SPC) | Y | Y | Y | Y | Y | Y | N |
| Replicate and sample SPC | Y | Y | Y | Y | N | N | N |
| Normalize by internal standards | Y | Y | Y | Y | N | N | N |
| NSAF Nrmalization | Y | Y | Y | Y | N | N | N |
| Spectral count Nrmalization | Y | Y | Y | Y | Y | Y | N |
| Apportion shared peptides by uniqueness | Y | Y | Y | Y | N | N | N |
| ANva significance test | Y | Y | Y | Y | Y | Y | Y |
| iTRAQ quantification | N | Y | Y | Y | Y | Y | N |
| TMT quantification | N | Y | Y | Y | Y | Y | N |
| Create custom isobaric labels | N | Y | Y | Y | N | N | N |
| Multiplicity support | N | Y | Y | Y | Y | Y | N |
| Internal and external replicates | N | Y | Y | Y | Y | N | N |
| Correction factors | N | Y | Y | Y | Y | Y | N |
| Control reporter ion peak picking | N | Y | Y | Y | Y | Y | N |
| Modify reference group selection | N | Y | Y | Y | N | N | N |
| Intensity based Nrmalization | N | Y | Y | Y | N | N | N |
| Validate reportor ion intensity | N | Y | Y | Y | Y | Y | N |
| Quantify by SILAC | N | N | Y | Y | N | Y | N |
| Support for ICAT | N | N | Y | Y | N | Y | N |
| 15N and 18O workflows | N | N | Y | Y | N | Y | N |
| Create custom isotopic labels | N | N | Y | Y | N | Y | N |
| XIC visualization | N | N | Y | Y | N | N | N |
| Interactive precursor scans | N | N | Y | Y | N | N | N |
| Baseline detection | N | N | Y | Y | N | N | Y |
| S/N detection algorithms | N | N | Y | Y | N | N | Y |
| Peak smoothing | N | N | Y | Y | N | N | Y |
| Manual peak integration | N | N | Y | Y | N | N | N |
| Intensity based label free quantification | N | N | N | Y | N | N | Y |
| Robust peak alignment | N | N | N | Y | N | N | Y |
| Support for fractionation workflows | N | N | N | Y | N | N | N |
| Customized precursor selection | N | N | N | Y | N | N | N |
| Support for high resolution data | N | N | N | Y | N | N | Y |
| Support for low resolution data | N | N | N | Y | N | N | Y |
| Manual peak area selection | N | N | N | Y | N | N | Y |
| Peptide and protein label free quantification | N | N | N | Y | N | N | N |
| Thermo Scientific™ MS file support | N | N | Y | Y | N | Y | Y |
| ABI MS file support | N | N | Y | Y | N | N | N |
| Maximum file limitations (64bit OS) | 30K peptides /GB RAM | 30K peptides /GB RAM | 30K peptides /GB RAM | 30K peptides /GB RAM |
ProteoIQ® is a comprehensive suite to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. With dynamic extracted ion chromatogram plots, the ability to view every MS spectra at any time point and the ability to manually select a peak area, ProteoIQ® provides the ultimate level of control.
ProteoIQ® provides a completely customizable interface to support any form of biological annotation. You can easily compare protein quantitative results in relation to biological pathways, protein localization, protein function, or even compare to transcript abundance. Every protein identification in ProteoIQ® can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or even an in-house LIMS.