Specifications

Data Import | Run Alignment | Analysis and Review | Advanced Statistical Analysis
Protein Identification | Reporting | Export of raw measurements

 

Data Import Specifications

• Supports LC-MS data in profiled mode
  
• Supports standard formats
  
  • .mzXML
    
  • .NetCDF
    
  • zlib compression in .mzXML data
    
• Optionally supports LC-MS/MS data in profile or centroid mode (mzXML only)
  
• Add LC-MS run data from multiple folders
  
• Quality control check performed on data files as they are imported to ensure they are in the correct format for analysis
  
• Intelligent peak-modelling algorithm to remove background noise and reduce data file size. Peaks are identified and peak models created that retain all relevant quantitation and positional information.

 

Run Alignment Specifications

• Unique algorithm achieves scan level correction of retention time variation through the addition of alignment vectors
  
• Automatic placement of alignment vectors
  
• Assisted placement of manual vectors

Image Display

• Preset image enhancement options access a wide range of image intensity levels
  
• Automated contrast stretching using Enhanced Grid squares option

Alignment visualisation

• 4 simple integrated and interactive run image views on User Interface (UI)
  
  • Zoomed alignment view
    
  • Alpha blend view with auto zoom for accurate vector placement
    
  • Overlaid run images view
    
  • Zoomed Chequerboard view
    
• Quick, simple run image focus using one-click selection from displayed list
  
• Option to change alignment overlay colours
  
• Display alignment vectors
  
• Display aligned grid
  
• Tick / cross buttons to individually include / exclude runs from further analysis

Alignment controls

• Adjustable alignment focus grid size
  
• Automatic and manual control of positioning the alignment focus
  
• Systematic mouse/keyboard driven navigation of alignment focus
  
• Drag and drop placement of alignment vectors
  
• Show aligned view with option to:
  
  • Apply alignment change
    
  • Always show aligned
    
• Show unaligned to view vector length and orientation
  
• Flexible options for vector removal
  
  • Single vector removal by right mouse click
    
  • Remove automatic vectors in current square
    
  • Remove automatic vectors from the whole image
    
  • Remove all vectors in the current square
    
  • Remove all vectors

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Analysis and Review Specifications

Mask of disinterest

• Ability to draw a mask of disinterest which is excluded from the analysis
  
  • Exclude area outside rectangle
    
  • Exclude area within rectangle
    
  • Exclude area within an ellipse
    
• Ability to edit a mask of disinterest

Detection and quantitation of peptides

• Creation of aggregate run that includes retention time aligned peaks from all runs
  
• Automatic analysis of aggregate run data and same peptide outlines applied across all runs in the experiment
  
• Matching of all peptides across the experiment to create a complete data set
  
• Peptide abundance determined using total isotope peak volumes
  
• Robust median based normalisation to compare peptide quantitation between runs
  
• Ion charge, m/z and retention time associated with each peptide

Experimental group set-up

• Group runs according to experiment structure
  
• Ability to set up multiple experimental groupings, e.g. male v female, control v treated
  
• Name search facility to assist with group set up in large experiments
  
• Rename experimental groups
  
• Colour coding of experimental groups
  
• Ability to add and remove data files from experimental groups
  
• Ability to delete groups

Review peptides of interest

• Automatic highlighting of interesting peptides according to ANOVA p-values
  
• Peptides ranked by ANOVA p-value or fold change
  
• Switching between experimental groupings automatically updates all views
  
• Peptide ID numbers remain consistent when experiment groupings are changed
  
• Tick / cross buttons to individually include / excluding interesting peptides
  
• Click and drag to select multiple peptides to be ticked / crossed
  
• Notes field for each peptide
  
• Visible count of number of peptides ticked / crossed
  
• Automatically advance through peptide list

Peptide tags

• Colour coded tags to assist with data exploration
  
• Right click on highlighted group of peptides to tag
  
• Add name label to peptide tag
  
• Filter peptide list by tags
  
• Tag editing
  
• Peptides can be tagged multiple times
  
• Peptide tags maintained throughout the workflow

Viewing options

• Colour coding of peptide outlines to indicate ion charge
  
• Edit ion charge colours
  
• Select an individual run or the aggregate for display
  
• Whole run image view
  
  • Click and drag to control zoomed view range
    
• Zoomed run image view
  
  • Click and drag to explore run at any resolution
    
  • View detected peptide outlines in detail
    
  • Click to select peptide and zoom
    
• 1D view
  
  • Mass spectrum of selected peptide
    
  • Selected ion chromatogram for selected peptide
    
  • Click in zoomed run image view to change mass spectrum and chromatogram focus
    
  • Mass spectrum and chromatogram ranges automatically adjust to match zoomed run image view
    
• 2D montage view
  
  • Show current peptide or all peptides
    
  • Adjustable contrast
    
  • Adjustable montage view size
    
• 3D montage view
  
  • Select runs for showing in 3D
    
  • Show current peptide or all peptides
    
  • Click and drag to reposition 3D view
    
  • Rotate option
    
  • Adjustable peak scale
    
  • Contour display option (where supported by graphics card)
    
• Expression profile view
  
  • Plot of mean log transformed normalised volume for each experiment group
    
  • Error bars showing 3 standard errors within groups

Peptide editing tools

• Peptide edit performed on a single run propagated across all the runs in an experiment
  
• Editing tools:
  
  • Edit peptide
    
• Add isotope
  
• Remove isotope
  
• Adjust isotope bounds
  
  • Split peptide
    
  • Merge peptides
    
  • Delete peptide
    
  • Add peptide
    
• Undo / redo peptide editing
  
• Automatic recalculations and update of measurements table following editing
  
• Single click recalculation of peptide ranking by ANOVA p-value following editing

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Advanced Statistical Analysis Specifications

Further statistical analysis of spots of interest

• Calculation and display of q-values for indication of False Discovery Rate (FDR)
  
• Calculation and display of peptide power
  
• Selected peptide(s) shown in standardised expression profile view
  
• Selected peptide(s) highlighted on Principal Components Analysis (PCA) plot
  
• Peptide tags can be added and are maintained throughout the workflow
  
• Filter peptide list by tags and all views are automatically updated

Principal Components Analysis

• Calculate principal components for all groups
  
• Calculate principal components for a selection of peptides
  
• Graphical visualisation of calculated components with groups highlighted for visual confirmation of clustering
  
• Selection of principal components to display on axis
  
• Zoom functionality

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Protein Identification

• Integration of MS/MS ion search via export of peak lists to third party protein identification software (for data files containing MS/MS scans only)
  
• Support for
  
  • Mascot (export .mgf and import .XML files)
    
  • SEQUEST (export .dta and import .out or .pepXML files)
    
  • Phenyx (export .mgf and import Progenesis.tsv files)
    
• Automatic matching of MS/MS scans to detected peptides
  
• View of MS/MS precursor m/z and retention time on detected peptide outlines
  
• Graphical view of MS/MS peaks
  
• Selection of spectra to export individually or by group
  
• Imported protein identification information is automatically linked back to detected peptides

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Reporting

• Export of inclusion list
  
• Whole run view showing locations of selected peptides
  
• Peptides selected for reporting using tag filtering
  
• Information for each selected peptide:
  
  • m/z
    
  • charge
    
  • retention time
    
  • peptide notes
    
  • Protein ID score table
    
• 2D montage view showing peptide outlines
  
• Peptide expression profile showing mean log transformed normalised volume for each experiment group and error bars showing 3 standard errors within groups
  
• Print and save report
  
• Open report in new window
  
• Customisable experiment report

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Export of raw measurements

• Export of peptide measurements as csv (commas separated value) file via File menu
  
• Select values to export for each peptide from
  
  • ID number
    
  • m/z
    
  • Retention time
    
  • Charge
    
  • Maximum fold-change
    
  • ANOVA p-value
    
  • Included (ticked or crossed)
    
  • Normalized abundance
    
  • Raw abundance
    
  • Tags selected
    
  • Protein score table
    
  • Best peptide match
    
• Score
  
• Protein
  
• Sequence