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Local FDR-Based Peptide Scoring x mzIdentML 1.1 Export for PRIDE xOn-the-fly Discriminatn Score Calculation x mzIdentML Support for Unknown Search Engines xFDR Protein and Peptide-level Filtering x Peaks 6.0 and Higher (*.mzIdentML) xFDR Landscape View for Optimizing FDR Levels x Myrimatch (*.mzIdentML) xProtein Family Clustering x SQID (*.mzIdentML) xImproved Protein Probability Weighting System x MS-GF+ (*.mzIdentML) xNew Quantitation Options: x MS-Amanda Support with Proteome Discoverer x

emPAI x Customized Unimod Modification Support x NSAF x Bulk Operations (Starring/Hiding/Exporting) xWeighted Spectrum Count x Multiple Star Color Categorization xFold-Change by Category x Sample Level Quantitation for Large Experiments x x

GO Annotation Filtering by Pie Charts x Statistical Blocking for Peptide Quantitation x xCategorical GO Term Quantitation x Peptide Level Label Free MS1 Precursor Intensity x xMaintain Multiple GO Annotation Databases x SILAC using SpectrumMill x

Mascot (*.dat) x x CID, ETD, HCD, ECD x x x xMascotDistiller (*.rov/*.xml) x xProteome Discoverer (*.msf) x x x Spectrum Mill (Results Directory) x x xSEQUEST (*.dta/*.out, *.ms2/*.sqt, *.srf) x x Phenyx (*.scaffold-pidres.xml) x x IdentityE/PLGS (*.xml) x Label Free MS2 TIC xX! Tandem (*.xml) x x Label Free MS2 Spectrum Counting x xOMSSA (*.omx) x x iTRAQ x x xMaxQuant/Andromeda (Results Directory) x x TMT x x xmzIdentML formats: x SILAC x x

Scaffold 3.1 and Higher x Site Specific Peptide PTMs xMascot 2.3 and Higher xPeaks 6.0 and Higher x

Time Course Experiments x x x xReference Based Experiments x x x

Peptide Prophet / Protein Prophet x Parametric Statistics x x xFDR Calculation at Peptide and Protein Level x T-Test x x x High Mass Accuracy Correction x ANOVA Test x x x Create Reverse FASTA Database x Fold change x x x Decoy Highlight Feature x Coefficient of Variation x x x X! Tandem Automatic Confirmation x Fisher's Exact Test for Spectrum Counting x Multiple Search Engines x Non-Parametric Statistics x xManual Validation x Mann Whitney Test x xPTM Site Localization with Ascore x Kruskal Wallis Test x xPTM Site Probability Estimation x Permutation / Bootstrapping x xPTM Motif Validation x Bonferroni Correction x x

Kernel Density Function Analysis x xIntensity Weighting and Error Estimation x x

MS/MS Spectra x x x xProtein Sequences with Overlayed Modifications x xProtein Coverage with Differential Expression x x Protein Probabilities xVenn Diagram (Proteins/Peptides/Spectra) x Peptide Probabilities xGene Ontology (GO) Annotation Frequency x Minimum Number of Peptides x Search Engines Scatterplot Comparisons x Peptide Sequence xROC (# identified spectra vs false positive rate) x Search Engines Scores xProtein Probability Calculation x Charge xMedian Kernel Density Separation x x Parent Mass Accuracy xRaw Intensity Distribution x x Number of Tryptic Termini xProtein Level Nomalized Intensity Scatterplot x x x Custom Modifications x x xPeptide Level Nomalized Intensity Scatterplot x x Protein Name x x xProtein Quantitation Charts x x x Fold Change x xPeptide Quantitation Charts x x Signal to Noise x x Sample Wide Fold Change Between Channels x x PTM Sequence Motif x xIntensity Weighting and Error Estimation x x Modification Site Probability xRandomized Permutation Calculation x x Summarization to Biological Sample Level x x x xMotif Sequence Visualization x Summarization to Biological Category x x xSite Localization Specific Barcode Charts xAscore Calculation Accuracy x

Windows 7, Vista, XP, 2000 x x x xWindows Server 2003/2008 x x x x

Free Viewer x x x x Mac 10.6 (Tiger) and Higher with 64 Bit Kernel x x x xFree 14 Day Trial at www.proteomesoftware.com x x x x Linux (Fedora, Red Hat) x x x xMeet Journal Standards (MCP Publishing Guidelines) x x x x 32-Bit Operating System Support x x x xCustomization of Available Views x 64-Bit Operating System Support x x x xPassword Protection of Saved Files x

Share and Publish

Label Free MS1 Precursor Intensity (AUC, Area Under the Curve) x

Search Engines Fragmentation Types

Quantitation

Differential Expression

Filter

OS Compatability

Validation

Visualization

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