myProMS
latest

Getting Started

  • Installation
    • Git Repository
    • Docker deployment
  • Login
  • Server Architecture

Server Management

  • Users management
    • User classes and access privileges
    • Account management
  • Annotation data management
    • Sequence databanks
      • Databank types
      • Listing databanks
      • Adding a new databank
      • Editing a databank
      • Deleting a databank
    • Spectral (SWATH) libraries management
      • Listing spectral libraries
      • Adding a new library
      • Merging two library
      • Editing a library
      • Updating a library
      • Restoring the previous version of a library
      • Searching for proteins in a library
      • Exporting a library
      • Deleting a spectral library
    • GO files management
      • Ontology files
      • Annotation files
    • Species
      • Listing species
      • Adding or editing a species
      • Deleting a species
      • Sequence modifications
    • Editing or merging PTMs
  • Server administration

Project management

  • Projects settings
    • Selection
    • Creation
    • Accessibility
    • Organization
      • Experiments
      • Samples
      • Analyses
    • Navigation
    • Life span
  • Analysis import
    • Supported search engines
    • Collecting search files
    • Import parameters (Mascot, Proteome Discoverer and X!Tandem)
    • Importing MaxQuant data
    • Import DIA data
      • From PeakView
      • From OpenSWATH
      • Running OpenSWATH quantification
      • From Spectronaut
    • Analysis summary
  • Analysis validation
    • Automated peptide/protein validation
      • FDR (False discovery rate) - based validation
      • Qualitative validation
      • Comparative validation
      • Validation templates
    • Manual peptide/protein validation
      • Peptides selection/exclusion
      • Protein exclusion and filtering
    • Lower-scoring peptides activation
    • Clear peptide/protein selections
    • Sequence modification validation
      • Phosphorylation sites validation with PhosphoRS
      • Manual validation of modifications
    • Validation traceability
    • Reporting
  • Biological Samples
    • Properties
    • Treatments
    • Recording a biological sample
    • Linking biological samples to MS Analyses

Protein Identification

  • Validated proteins
    • Match groups and protein visibility
      • Top protein selection rules
      • Project-wide protein visibility rules
      • Checking for conflicting match groups
      • Displaying match group composition
      • Manual edition
      • Peptide distribution in match group
    • Identifier mapping
    • Single protein view
  • Protein lists
    • Project-based protein lists
    • User-defined protein lists
    • Export protein lists
  • Search for proteins
  • Compare project proteins
    • Full protein-level comparison
    • Pairwise protein-level comparison
    • Pairwise peptide-level comparison
    • Saving a comparison

Quantification

  • Peptide Quantification
    • Data import from search results file
    • Data extraction from LC/MS file with MassChroQ
      • Managing mzXML files
      • Running XIC extraction
    • Virtual/Ghost peptides and proteins
    • Displaying peptide quantification data
  • Protein Quantification
    • Absolute abundance quantification
      • emPAI (label-free)
      • SIn (label-free)
      • MaxQuant: Intensity, LFQ, iBAQ
      • Proteomic Ruler
      • Displaying single abundance quantification data
    • Relative abundance quantification
      • Single-Analysis quantification (labeled)
      • Design-based quantifications
      • Displaying relative abundance quantification data
    • Label-free quantifications
      • TnPQ
    • Comparing multiple protein quantifications
    • Exporting multiple quantifications
  • PTMs quantification
    • Set PTMs relevance to project
    • Display modification sites distribution
    • Compare PTMs between projects
    • Quantify modification sites

Data Analysis

  • Exploratory analysis
    • Launching exploratory analyses on protein quantification
    • Launching exploratory analyses on peptides count
    • Principal Component Analysis (PCA)
      • Summary / edit / delete
      • Displaying a PCA
    • 2D-Clustering
      • Summary / edit / delete
      • Displaying clustering
  • Functional analysis
    • Gene Ontology
      • GO summary
      • GO enrichment analysis
      • Quantitative gene enrichment analysis
    • Pathway enrichment
      • Launch pathway analysis
      • Summary / edit / delete
      • Displaying pathway analysis
      • Export
    • Motif enrichment analysis
      • Launch analysis
      • Summary/editing/deleting
      • Displaying motif enrichment
      • Heatmap motif analysis
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© Copyright 2019, Patrick Poullet, Valentin Sabatet, Victor Laigle Revision ea3c4e35.

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