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Full release note with fixes issues is available on project management web application (using RedMine).

hEIDI 1.14.3

Released on 26/MAR/2013

Bug fix : Distribution problem. hEIDI distribution without embedded JRE is now OK.

hEIDI 1.14.1

Released on 25/JAN/2013

  • Add Context ID in the property sheet (needed for imoprting spctrum using Paloma)
  • Change advanced spectral count output to allow better copy/paste into Excel

hEIDI 1.14.0

Released on 15/JAN/2013

hEIDI 1.14.0 is based on MSIdb E.2

  • Algorithms
    • Adjusted Spectral count : Add new spectral count Algorithm which calculate peptides SC weight on a parent context before calculating SC on child context.
  • Bugs Fixes :
    • Pride export on context with small name
    • AMT db export with peptide sequence greater than 50

hEIDI 1.13.0

Released on 29/FEB/2012

hEIDI 1.13.0 is based on MSIdb E.2

  • Algorithms
    • Context comparison
      • In the context comparison result view, 3 new columns have been added (to have these columns, there is NO need to run the spectral count algorithm on the compared contexts, prior to the comparison algorithm)
        • refLoc: can be [TYPICAL] or [SAMESET] or [SUBSET] or []. This field indicates where the typical reference was seen in the aligned protein group
        • refSC: this field indicates the Spectral Count value of the protein reference in the aligned protein group
        • refSpeSC: this field indicates the specific Spectral Count value of the protein reference in the aligned protein group
      • A dialog message has been added to confirm the MSIdb is saved before launching the comparison algorithm
      • The contents of the context comparison result table can be quickly saved to a .csv file.
    • Spectral count
      • Spectral count algorithm has been tuned and is really faster. To achieve this, MSIdb E.1 model has slightly changed (new peptide_leaves_count field in peptide_match table)
      • Spectral count on non-grouped context can not be run
    • False Positive Rate
      • False Positive Rate (in percentage) can be computed for a given User context and saved as a property. Formula used is: FPR=FP/(TP+FP) with FP=(2*reverse) and TP=(reverse+forward)-FP. The “significant.and.duplicated.fp” & “” properties are extracted from leave identifications falling under the given User context. If at least one of these properties is equal to zero, the concerned identification(s) is(are) not taken into account in the FPR calculation and user is informed)
    • Batch
      • Some algorithms can now be run in batch for multiple contexts: peptide/protein grouping, filtering, spectral counting
  • AMT
    • UMCs to MSIdb
    • A new wizard is available to import multiple UMCs result files (i.e. conglomerate files) into MSIdb. Each conglomerate file (i.e. each file containing UMCs) will result in a new Quanti context. Quanti context name is built from conglomerate filename and sample name (if found from ePims WebService) . A Quanti context contains identified/quantified peptides; the new peptide property “max abu” gives the maximum abundance for this peptide
    • AMTdb export enhancement (how-to)
      • Before exporting a context to an AMTdb, user is asked for analysis duration and delay. These 2 information, used to compute NET values, are stored in AMTdb (so AMT database model has slightly changed)
  • Peptide view
    • The m/z, delta m/z and retention time of the best child peptide are used when creating a new grouped peptide (ATTENTION: effective for the new grouping only!
  • Export (how-to, concept)
    • In the “Protein groups with peptides & leaves” custom export:
      • 2 new fields have been added: charge & score for leave peptides
      • export is customizable (user defines column visibility)

hEIDI 1.11.1

Released on 01/AUG/2011

hEIDI 1.11.1 is based on MSIdb E.1

  • Minor changes:
    • disabled 2 menus (Clear duplicated PTMs in MSI + populate MSI with spectra)

hEIDI 1.11.0

Released on 22/JUL/2011

hEIDI 1.11.0 is based on MSIdb E.1

  • Algorithms
    • Protein Grouping TUNED (but need the MSIdb to be saved preliminary)
    • Fixed a bug in Protein Grouping related to Database retrieval
    • Fixed a bug in “Change typical protein” algo
  • Export
    • Fixed a bug in “Same Subset Details” report

hEIDI 1.10.1

Released on 08/MAR/2011

hEIDI 1.10.1 is based on MSIdb E.1

  • Pride Export
    • Fixed bugs & enhanced .xml formating to be conform to PRIDE requirements + changed WIKI pages (Redundant PTMs, null ion parent intensity, redundant spectrum in leucine/isoleucine case, wrong m/z for precursor, wrong spectrumRef for precursor, no fragment matches in leucine/isoleucine case, wrong SearchEngine, wrong fragment match count, shortened databaseVersion, changed place for parent charge, added fragment ion annotations, skipped masked proteins/peptides)
  • Database
    • User can populate MSIdb with spectrum details (spectra & fragment matches)

hEIDI 1.10.0

Released on 01/FEB/2011

hEIDI 1.10.0 is based on MSIdb E.1

  • Algorithms
    • “Compare each other”/“Compare with children” algorithms and their different result windows are now replaced by a unique algorithm/Result window. As well, multiple contexts, even without any parent/children relation can be compared to their union
    • You can now recompute retention time, in one pass, for the selected User context and all of their child contexts
    • Filtering (i.e. masked peptides/proteins/protein groups) can be reset for one or several selected User context(s) and optionnaly for all of their child contexts
    • Fixed a bug regarding “peptide count” filter, when specifying only a number of peptides
    • Fixed a bug regarding all filters (they applied systematically to all child contexts instead of the selected context)
  • Export
    • Progress bar added when exporting to AMT database
  • hEIDI Project
    • Close all opened windows when an hEIDI Project is disconnected from its MSIdb. Memory is released
  • Peptide view
    • Workaround for duplicated PTMs in peptide view (#1929) (while waiting for a more robust SQL fix)

hEIDI 1.9.0

Released on 28/OCT/2010

hEIDI 1.9.0 is based on MSIdb E.1

  • MSI database
    • New E.1 MSIdb model is partially supported (quantitation information, for instance, is not yet visible in hEIDI but nevertheless, user can query quantitation tables using SQL)
  • Peptide view
    • Fixed a bug when displaying masked peptide in a filtered context
  • Algorithms
    • You can compare a external list of accession numbers with all proteins of a selected context

hEIDI 1.8.0

Released on 12/OCT/2010

hEIDI 1.8.0 is based on MSIdb D.3, but D.4 is required if your are using PRIDE XML Export

  • Export
    • A Context can now be exported into PRIDE XML format

hEIDI 1.7.0

Released on 10/SEP/2010

hEIDI 1.7.0 is based on MSIdb D.3

  • Identification view
    • Sample & Study names can now be displayed in the identification window using the 'fill sample information' menu
  • Peptide view
    • Added “Typical(s) Matching” column to display the number and the accession of master protein matches
  • Algorithms
    • Context comparison has been modified: when 2 Protein Groups have a same (even 0) peptide similarity, their protein similarity is taken into account. If the protein similarity is the same as well (with a non-zero peptide similarity), All Protein Similarity is used to discriminate the two groups
  • Reporting
    • 'Protein Group Details' report:
      • Added the “#Master protein matches:Master protein matches” column
      • Added the number and list of PTMs
      • Removed the “state” column
    • 'Peptide Details' report:
      • Changed the “#Master protein matches:Master protein matches” column to only display accession for typical protein matches
  • Context saving
    • Correct end message when context saving has failed
  • MSI Database
    • Increased size of 'name' field for 'property_group' table

hEIDI 1.6.1

Released on 04/AUG/2010

hEIDI 1.6.1 is based on MSIdb D.3

Fix urgent issues.

hEIDI 1.6.0

Released on 03/AUG/2010

hEIDI 1.6.0 is based on MSIdb D.3

  • Data
    • Run & Sample information can be automatically retrieved from ePims WebService
  • Algorithms
    • Protein grouping is memory tuned
    • Retention Time Alignment
    • Retention Time Recomputing
    • Compute spectral count for proteotypic peptides only
  • AMT database
    • UMCs from several Conglomerate files can be included in AMT database
    • Removed wrong 1-N relationship between AMT_Proteins & protein_to_protein_group_map tables
    • Added new field descriptions for AMT_Proteins, protein_group & protein_to_protein_group_map tables
  • Peptides view
    • Navigating through child species from a given species node is now possible
    • Added a new column: # of distinct identifications where the peptide has been seen
  • Reporting
    • 'Peptide Details' report:
      • Added a column for protein accession
      • Size of 'Sequence' field has been increased
    • 'Summary' report:
      • Size of 'Description' field has been increased

hEIDI 1.5.0

Released on 27/APR/2010

hEIDI 1.5.0 is based on MSIdb D.3

  • Protein filtering / Peptide grouping criteria
  • Save of used parameters (as context properties) for the following operations: “Change typical protein”, “Species/Protein Grouping”, “Putative protein filtering”
  • New reports:
    • Sameset and Subset proteins for each protein group
    • Peptide list
  • Ascending order of child contexts

hEIDI 1.4.0

Release date : 29/01/2010 Summary

See all issues on redmine project

Features : - Projects managment - Contexts Comparison result backup - Visualisation of peptides hierarchy - spectral count bugs (none display value, empty export…) - AMT export in new database model.

hEIDI 1.3.0

Released 09/17/2009


  • Change table row default height
  • Comparison
    • add custum multiple contexts comparison table.
    • add dynamically generic properties (spectral count…) to multiple context comparison table


  • Add graphical reports view for selected contexts' peptides
  • Enable protein grouping on proteins imported with CSV file.
  • Enable Identification properties edition


  • Export AMT bug fixe : Protein description column was too small.
  • Dynamic report export bug fixe.

hEIDI 1.2.0

  • Multiple contexts comparison
    • from common root context
  • Results export
    • Read Viper output and save data in AMT db
    • Display PTMs in peptides list
    • Action management
      • Confirmation / error message dialogs
      • Uses ProgressBar for long actions

hEIDI 1.1.0

  • Add spectral count module
  • Peptides views
    • Peptide detail : allow multiple windows to see many peptides descriptions in the same time (uses pin feature to freese windows)
    • Context's peptide list
  • Proteins view
    • Allow multiple window (using pin feature)
    • Context's proteins list
  • Export
    • Export a context into AMT db format
    • Export 2 contexts comparison result
    • Add a customizable context export
  • Features added
    • Remove “Search” Context
    • Save “User” contexts back to MSIdb
  • Update properties displaued for identification, proteins, peptides..
releasenotes.txt · Last modified: 2013/03/26 08:14 by