Opened 4 years ago

Last modified 4 years ago

#805 new task

Service lab: Annotation of MALDI peaklists

Reported by: Rene Ranzinger Owned by:
Priority: normal Milestone: Module - Service lab plugin
Component: Service lab plugin Version: GRITS 1.1.x
Severity: major Keywords:
Cc:

Description (last modified by Rene Ranzinger)

Ticket #806 is a prerequisite for this ticket.

  • Add a new menu entry in the service lab menu (no precondition for enabling): "Annotate MALDI data"
  • When choosing this menu entry - dialog appears with
    • File chooser to select Excel peaklist
    • A tolerance value (double) combined with a dropdown (values: ppm, Da)
    • Dropdown list with the names of the glycan databases in the preference (see #806)
    • File chooser for the output file
    • Dropdown to choose the output format (Word or Excel) -> This can also be part of the file save dialog ("Save as type" filter)
    • OK, Cancel button
  • When clicking ok
    • load the Excel file (two formats are shown in attachment (extended and normal version) - they can be distinguished by the first row)
      • Extract for each row the "Centroid Mass" and "Area" cells
    • Match the rows in the peak lists with the glycans from the selected database from the preferences
      • For each Centroid Mass value calculate the tolerance (+- Da value or +-ppm value divided by 1,000,000)
      • Search in the list of glycans for glycans with a mass that falls into the tolerance
      • If more than one glycan matches - present the centroided mass to the user and a dropdown with the different matching glycan compositions -> user chooses the glycan he wants to use from the dropdown + OK
    • Export the Peaklist - glycan match into a table (Word or Excel based on user choice)
      • An example file is attached (table.docx)
      • Columns
        • Mass = rounded centroid mass value from peaklist
        • Text description of structures = composition from glycan
        • Cartoon representation of structures = Image generated from the GWS sequence from the glycan (Sena has example code). If no GWS sequence is present for the glycan this cell is empty.
        • Area = Area from peaklist file
      • Save the file to the specified file location
      • There is example code for exporting images in Excel in the MS plugins (Sena and Brent) - important is to set the row hight to prevent miss alignment of the image with the rest of the row

Attachments (3)

Table.docx (52.3 KB) - added by Rene Ranzinger 4 years ago.
peaklist.xlsx (49.1 KB) - added by Rene Ranzinger 4 years ago.
peaklist-extended.xlsx (106.2 KB) - added by Rene Ranzinger 4 years ago.

Download all attachments as: .zip

Change History (8)

comment:1 Changed 4 years ago by Rene Ranzinger

Description: modified (diff)

Changed 4 years ago by Rene Ranzinger

Attachment: Table.docx added

Changed 4 years ago by Rene Ranzinger

Attachment: peaklist.xlsx added

Changed 4 years ago by Rene Ranzinger

Attachment: peaklist-extended.xlsx added

comment:2 Changed 4 years ago by Rene Ranzinger

Description: modified (diff)

comment:3 Changed 4 years ago by Rene Ranzinger

Description: modified (diff)

comment:4 Changed 4 years ago by Rene Ranzinger

Description: modified (diff)

comment:5 Changed 4 years ago by Rene Ranzinger

Milestone: GRITS - 1.2Module - Service lab plugin
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