Proline Release Notes

Version 1.5

  • New global features (on server):
    • LC-MS quantitation performance optimization and enhancement: lower memory consumption and faster quantitation processing
    • Export enhancement
      • Several bugs fixed (order of columns, MW&coverage, fix the computation of #PSMs/#Specific PSMs/#Sequences, support of decimals with comma separator)
      • Quantitative exports: keep sample order (same as specified in GUI)
      • Add some new columns: samesets/subsets accessions, gene name, PTM location on protein, number of observable peptides, observed m/z and corrected RT of each quantified ion.
    • Short services are treated separately. This prevent waiting fot connection, server browsing… when server is busy.
    • Determination of spectrum retention time
      • Update Spectrum using new Peaklist software : fixes issues in order to get RTInSeconds if no value found for Time
      • Fix a bug: RTINSECONDS was not taken into account when its value was zero
  • New features in Studio:
    • Add Folder in quantitation and identification tree
    • XIC dialog bug fixes and enhancement and separate simple vs advanced parameters
    • Ability to cancel server running tasks
    • DataAnalyzer
      • import CSV : automatic detection of the separator, preview of the file parsing, bug fixes when loading data from CSV
      • Enhancements for ProStar Macro : Graphical Selection of Thresholds, possibility to show Differential Proteins
      • New algorithm for Diff/join : possibility to have 2 keys and one of the keys can be a double value with tolerance.
    • Add Admin features (add/modify user; peaklist software…)
    • Raw/MzDB : Convert and/or upload on Server side
    • Bug fixes for Adjacency Matrices : memory problems, tasks not stopped
    • Observable Peptides column for validated proteins (need to potentially retrieve protein sequences)
  • New features in Web:
    • Set/Unset favorites in batch from table content (using table filters)
    • Clone a quantitation: open pre-filled form to launch a new quantitation
    • Utilities to copy all tables
    • Vizualize the parameters used for LFQ and post-processing
    • Fix user creation
    • Add organization folders in quantitation tree
    • Some enhancements in SpecLight XIC visualization
  • New features in MS-Angel:
    • Improve panel for input files
    • Add many checks for workflow validity, previous to task launching
    • Improve/fix task cancellation
  • New features in mzDB-Wizard:
    • New two-step opening dialog. In step 2 we can now select an existing mounting point based on the server selection done on step 1.
    • Possibility to restart failed task.
    • Check for corrupted files before running actions.
    • Add MGF export from mzdb files.
    • Task Manager : sorting is now possible ans more tasks’ details displayed.
    • User Interface changed ti be more user friendly
    • Documentation is accessible inside the application.
    • Logs: in GUI now contain date & time; Refined all messages and changed logfile names

Previous versions

Version 1.4

  • New global features (on server):
    • Quantitation Refine : new Abundance Summarizer method, Median Ratio Fitting
    • Filter : add Protein Set score filter
    • Export
      • Quantitation export : elution time and peptide number was wrong
      • Export Pride : explicit error when spectra are missing
    • Spectral Count : Fix error when parent identification summary was added in list of identification summaries to calculate SC for
  • New features in Studio:
    • Add a “General Settings” windows
    • Ability to view also Server Tasks Logs and to cancel user pending tasks
    • XIC Quantitation
      • experimental design : Drop Zone to automatically associated mzdb files to Identification Summaries
      • result could be refined by selecting/unselecting quantified peptides
    • New Data Analyzer, finished first integration of DAPAR (ProStar)
    • Navigation facility : added a popup option in all data tables to display complementary information.
      (Like adjacency matrix for a Protein, Identification data for XIC Protein Set…)
    • Enhanced Adjacency matrices : added selection of Proteins/Peptides
    • Export : change default value for ProteinSet list to export : Only validated by default
  • New features in Web:
    • Add a system for favorite entities
    • Add a tool to change sample names in batch using copy/paste from an Excel table
    • Add a tool to create a dataset on 2 or 3 levels using copy/paste from an Excel table
    • Improve information on quantitation result graphics (tooltips)
    • Add tables in quantitation viewers, replacing the protein set grouping system
    • Selection/deselection of a peptide at protein/dataset level
    • Ease the creation of the experimental design (improve drag and drop, display sample name)
    • Fix some display bugs, in particular toward tables rows filtering
  • About 50 issues closed…
  • New Tools are available in this Release
    • mzDB-Wizard: this tool allow user to easily convert raw files to mzdb (for XIC quantitation) and upload them on server side
    • MS-Angel: Provide a complex workflow, complete data visualization, real time monitoring, submission to many search engines (Mascot, OMSSA, X! Tandem: in progress).

Version 1.3

  • New global features (on server):
    • Algorithm and other operation
      • Faster datasets export
      • New service to clean up a project : remove unused identification data (Search Results or Identification Summaries put to trash or no more accessible to user, after re-validation for example)
      • New Quantitation Post-Processing options
      • Import MzIdentML result file
  • New features in Studio:
    • Allow to run “XIC” from a merged dataset. The identification summary associated to the dataset will be used as parent identification summary of quantified identification summaries.
    • XIC – experimental design : Change view to associate mzdb files to dataset
    • Simplify Mascot specific parameter in import
    • Integration of R package DAPAR(also interfaced with ProStaR)
  • About 40 issues closed…

Version 1.2

  • New global features (on server):
    • Algorithm and other operation
      • Fragment Match Generator for XTandem result.
      • FDR change : Use TD competition if rank filtering is used
      • XIC Enhancement
  • New features in Studio:
    • Menus’ reorganization (Identification and Quantitation)
    • New display of MsQueries (for a Search Result or an Identification Summary)
    • XIC: New display of experimental design and XIC parameters
    • XIC: New display of alignment map and calculating of predicted elution time
    • MzScope (mzDB file viewer) convert into MGF files, display of multi raw files, LCMS map viewer
    • Allow Fragment Match Generator to be called from both Identification & Quantitation Trees
    • Add spectra Library generation
  • New features in Web:
    • Customizable export of identification and quantification datatsets
    • Enhancement of quantification results visualization
    • Integration of Spectlight, a 3D web-viewer of mzDB files to manually check a peptide environment and its XICs over all input files
  • About 150 issues closed…

Version 1.1

  • New global features (on server):
    • Algorithm and other operation
      • Spectral Count algorithm modification: Spectral Count Weigth is based on specific PSM count instead of specific peptide count.
      • ProteinSets filtering (independently of validation)
    • Save, import and export ◦Export to PRIDE format
      • Support import of X!Tandem result file
  • New features in Studio:
    • Algorithm and other operation
      • Enhancement of data mixer: module to easily do calculations/comparisons on data.
      • Integration of a calculator: it lets you write python scripts to manipulate freely viewed data.
      • Add interface for ProteinSets filtering
    • Save, import and export
      • Customizable export of Identification dataset, or Spectral Count or XIC
      • Add interface for Export to PRIDE format
      • Add interface for import of X!Tandem result file
    • Display
      • Display MzDB Files through mzScope module (directly in Studio)
      • Enhancement of the XIC display and Spectral Count display
  • New features in Web:
    • New & improved Interface !
    • New data and chart vizualisations for quantitation stats