====== How to ======

:!: Current documentation corresponds to Proline Release 1.1 

Note: Read the [[..:prolineConcepts:start|Concepts & Principles documentation]] to understand main concepts and algorithms used in Proline.

===== Proline Admin =====


  * [[.:createUser|Create a Proline User]]
  * [[.:createProject|Create a Proline Project]]

===== Proline Studio =====

==== Creation/Deletion ====
  * [[.:studio:startSession|Open a session and access to my projects]]
  * [[.:studio:createProject|Create a new project]]
  * [[.:studio:createAggregate|Create a Dataset]]
  * [[.:studio:importmascot|Import a Search Result]]
  * [[.:studio:delIdf|Delete Data]] and clean project
  * [[.:studio:connectionMgmt|Connection Management]]
==== Display  ====
  * [[.:studio:viewPSM|Display MSQueries, Peptides/PSM or Proteins]] of a Search Result 
  * [[.:studio:viewProtSet|Display MSQueries, PSM, Peptides, Protein Sets, PTM Protein Sites or Adjacency Matrices]] of an Identification Summary
  * [[.:studio:RSproperties|Display Search Result & Identification Summary Properties]]
  * [[.:studio:viewSpectralCount|Display Spectral Counts]]
  * [[.:studio:viewXIC|Display XIC]]
  * [[.:studio:createuserdisplay|Create and Save a User Window]]
  * [[.:studio:Abbreviations|List of Abbreviations]]
  * [[.:studio:FrameToolbars|Frame Toolbars Functionalities]]
  * [[.:studio:filterTables|Filter tables]]
  * [[.:studio:searchTables|Search tables]]
  * [[.:studio:histograms|Graphics : Scatter Plot / Histogram]]
  * [[.:studio:MSDiag|Statistical Reports (MSDiag)]]
  * [[.:studio:MzScope|MzDB Files (MzScope)]]
==== Save, import and export ====
  * [[.:studio:importMascot|Import Mascot/OMSSA/X!Tandem result file]]
  * [[.:studio:exportData|Export data]]
  * [[.:studio:generateSpectrumMatches|Generate Spectrum Matches]]

==== Algorithm and other operation ====
  * [[.:studio:rsValidation|Validate a Search Result]]
  * [[.:studio:protSetFiltering|Filter Protein Sets]]
  * [[.:studio:changeTypicalProt|Change Typical Protein of a Protein Set]]
  * [[.:studio:merge|Merge]]
  * [[.:studio:datamixer|Data Analyzer]]
  * [[.:studio:calculator|Calculator]]
  * [[.:studio:newPeaklistSoftware|Update Spectrum using Peaklist software]]

==== Quantitation ====
  * [[.:studio:spectralCount|Spectral Count]]
  * [[.:studio:xic|XIC]]
  * [[.:studio:xicProfilizer|Refine Protein Sets Abundances]]

==== Other ====
  * [[.:studio:preferences|Preferences Dialog]]

===== Proline Web =====

==== Workflow ====

  * [[.:web:startSession|Open a session and access to my projects]]
  * [[.:web:regiserRawFiles|Register and pair Raw & MzDB files]]
  * [[.:web:createProject|Create a new project]]
  * [[.:web:importResultFiles|Import Result Files]]
  * [[.:web:createAggregate|Create an Identification Dataset]]
  * [[.:web:rsValidation|Validate a Search Result]]
  * [[.:web:createQuantitation|Create a Quantitation]]
  * [[.:web:delIdf|Delete Datasets]]

==== Users management ====
  * [[.:web:createUser|Create a User]]

==== Display  ====
  * [[.:web:RSproperties|Display Identification Summary information]]
  * [[.:web:viewProtSet|Display proteins sets]] in Identification Summary
  * [[.:web:viewPSM|Display peptides and/or PSM]] in identification result

  * [[.:web:quantitationResults|Display Quantition results]]



==== Save, import and export ====
  * [[.:web:exportData|Export data]]
  * [[.:web:importResultFiles|Import Result Files]]

====Algorithm and other operation ====
  * [[.:web:rsValidation|Validate a Search Result]]