Melanie 9.0.0 (2017.8.10.0)

This page describes the new features, changes and fixes that were introduced in the Melanie software since the release of Melanie 8.0.1 (2016.7.6.0).

New features

Coverage module (HCP Antibody Coverage Analysis)

  • Completely new module with workflow and tools dedicated to the analysis of 2D-PAGE based HCP antibody coverage.
  • Multiple HCP antigen / anti-HCP antibody image pairs can be analyzed as part of the same experiment.
  • Three-level spot filter to categorize spots on each image as absent, present or uncertain based on spot abundance thresholds.
  • Easy review of spot coverage status using 3D view.
  • One-click edit of spot coverage status in images or table.
  • Coverage results displayed as Venn diagram, Spot count or Histogram.
  • Choice of coverage formula (3 options) for each of 3 coverage types.
  • View coverage for different targets (subsets of spots).
  • Create and manage different coverage pairs.
  • Customizable coverage summary histograms to compare results from different coverage pairs.

Classic and DIGE modules (Differential Protein Expression Analysis)

  • Principal component analysis (PCA).

Classic, DIGE and Coverage modules

  • Dedicated interface to define pI and MW markers (for subsequent calculation of theoretical pI and/or MW values for all spots).
  • Spot editing in 3D view (in addition to 2D view).
  • Numerical fields, spot sets and annotations in tables can be displayed as spot labels on the images. Such labels can be displayed on all spots, selected spots (adaptive) or presently selected spots (fix).
  • Spots can be color-coded in images and tables based on a numerical field or spot set, using customizable color palettes. This notably allows easy visualization of under- and over-expressed spots.
  • Menu icon for quick access to projects and export options.
  • And more…

Changes

Alignment setup

  • In a project of type Multiple stain without internal standard, it is now possible to choose/change the reference image for each gel by dragging the desired reference image into first position.

Alignment

  • Improved alignment efficiencies.
  • Match percentage is now calculated as the number of matches relative to the number of spots in the reference image.
  • For DIGE experiments, the spots of the internal standard image are now always projected on the aligned image.

Detection

  • Spot detection parameters can be entered manually, in addition to using the slider.
  • Maximum limit for Min area has been increased to 150 in Detection parameters.

Review – Spot filter

  • For DIGE data sets, internal standard images are now included in the Group table and Selection criteria when using a quantification value other than Vol ratio.

Review – Spot edition

  • Redesigned spot editing tools.

Review – Spot normalization

  • Filter by values has been enabled in the Normalization table.
  • Y-axis of the Normalization plot has been made symmetrical.

Results

  • For DIGE data sets, it is now possible to display a Gel analysis on all images including the internal standard images or on the internal standard images only. In these cases, the Expression profile and Group table display Vol instead of Vol ratio.

Display area

  • Improvements in the 3D view.

Image view

  • Image order in the Display area is now preserved when deselecting/reselecting images in the list.
  • Spot selection behavior has slightly changed so that a selected spot remains selected on the other images when an image is deselected for viewing.

Annotations, spot sets, validation columns

  • An annotation category can now be deleted directly.

Performance and usability

  • Redesigned printing tools.
  • Enhanced sorting symbol on column headers.
  • Improved management of locking / unlocking projects for edition.
  • Numerous small terminology changes to improve consistency.
  • Reworded warning and error messages to improve clarity.

Fixed bugs

Quality control

  • File management issues when renaming or deleting images.
  • When, on an analyzed project, an image was excluded, and then again included (after having reanalyzed the data set), the display of spots on this image became inconsistent (no spots appeared on the image in Spot edition).
  • Percentage of saturated areas and background clipping in the table were erroneous for some calibrated images.
  • Percentage of background clipping in the table could change for certain images when going to Edit images and then coming back to the main Quality control screen.
  • After contrast adjustment and edit of images in Edit images, the contrast adjustment was not applied to the edited images (starting from the Experiment design step).
  • In Adjust contrast, in Edit images, when switching color palette (Colors) when several images were open, the color palette was not correctly applied.

Alignment setup

  • Saving of groups failed when there were dots in the image file names.

Alignment

  • For DIGE experiments, when the Intra (DIGE) align option is unticked in the Workflow options, it was possible to carry out individual within-gel alignments and violate the 100% matching rule.
  • For some images, typically images with very high resolution, the software could become unresponsive during the Alignment. This was caused by the default spot detection parameters (for the Alignment step) generating too many spots, thus negatively impacting alignment efficiency and speed. The software now shows a warning message when the number of spots in the alignment is too high, and gives the possibility to adjust the detection parameters in Workflow options.
  • Crash after Undo of an automatic alignment if preceded by a specific sequence of alignment editing steps.
  • Grid was not always correctly initialized when switching between images that were at different levels in the alignment hierarchy.
  • Alignment status of some images in the Tree view could be inconsistent following alignment on multiple images.

Detection

  • Crash on choosing Ignore modifications when leaving the Detection step after modifying detection parameters, when the project contains spots selected for picking.
  • Spots were not re-detected after editing an alignment, then selecting a next alignment pair, before going to Detection. As a consequence, the 100% matching principle could be violated.

Review – Spot edition

  • Crash when deleting spots when not all images were selected.
  • Crash when moving spots outside the image area (more particularly at the top and bottom of the images).
  • Under some specific circumstances (depending on initialization settings for multi-threading), it was possible to create spots that fell outside the image area of some gels (and were therefore absent on those gels).

Review – Spot normalization

  • Filter by values did not manage the case where the value entered for the ‘>=’ criterion was larger than the value for the ‘<=’ criterion (to select spots at the top and bottom of the plot).
  • For DIGE data sets, only the internal standard images were sorted when clicking on a column header in the Normalization factor table.
  • Negative values were not correctly sorted when clicking on a column header in the Normalization factor table.

Results

  • Editing the Name and Comment of an analysis did not update the name of the corresponding analysis tab and the new Name and Comment were not appropriately restored after closing/reopening the software.
  • No analysis could be displayed/created after all factors in the Experimental design were removed (in a previously analyzed project).

Picking

  • Match vectors were drawn over the Ettan marker annotations.

Display area

  • In the Display area, image positions are no longer synchronized after quitting Spot edition without applying the edition.

Image view

  • Layout settings were not available in Image view when opened from Alignment or Picking.
  • Spot table in Image view did not display the Vol ratio column for DIGE data sets.

Annotations, spot sets, validation columns

  • Spot sets were reset (all spots unticked) after quitting Spot edition without applying the edition.

General

  • For images with a Transfer table, the minimum and maximum pixel values in Adjust contrast and Cursor information were inconsistent with the minimum and maximum values in the Quality control table. Please note that images are displayed in their calibrated form. Due to the rounding operations that this requires, small differences can persist between the strictly correct minimum and maximum values in the Quality control table, and the rounded values in Adjust contrast and Cursor information.
  • Error when reopening a project that used a Min area greater than 100 in the Detection parameters.
  • Export of image signatures didn’t work in Experimental design and Alignment setup steps for DIGE and Multiple stain without internal standard projects.