Software-SummaryCombinationProteinReport

1. Once report is finished for experiment, it must be added to the summary table.
2. The same experiement is repeated with 10 different samples and we create a spreadsheet reporting the proteins identified and their relative abundance in each.
3. The Excel file SummaryReportGenerator.xls is used for this.
4. Copy the worksheet from your Result file by right-clicking on the sheet tab, clicking 'create a copy' and selecting the SummaryReportGenerator.xls from the drop-down menu. Once the worksheet is in SummaryReportGenerator, select all, copy, and paste special, as values into a blank sheet (Sheet1) cut the extra columns so only 4 Columns are left: Accession, Description, iTRAQ Ratio and RSD. Rename Sheet1 to 'BM-164' or appropriate name.
5. Run Macro "ConciseFormatCombine" - All 15 worksheets of the repeated experiements are sorted one-by-one and added one-by-one into a large summary table in the worksheet "combination". When the macro completes in 10-20 seconds, activate the Combination sheet with the new table and select all by either selecting- edit, select all or clicking the upper left box at the juncture between 1,2,3 and A, B, C. Copy and paste special as values. Click on Column A, hold down shift and Click on the last column, for example Z. Copy then activate the sheet 'Normalize' and again click on A then hold down shift and select Z (the same number of columns as currently in the clipboard) then paste special as values.
6. Columns BA, BB, BC, BD, BE etc.. are formulas based on Columns A, B, C etc... with Protein-level normalization applied. The protein-normalization factor from the concise protein-list experiment report is used to adjust the protein's iTRAQ ratios so that the median of all iTRAQ ratios from proteins identified in the experiment will end up being 1.0
7. It is important that subsets of homologous proteins not be included in the list of proteins because this can skew the median if, for example there are lots of Keratins, IGg, Serum Albumin, etc.. these will affect the median causing a bias toward the over-reported protein.
8. With the protein-level normalization applied the summary report exists from Column BA through BZ. Highlight these columns, copy and paste special-as values into a new sheet.
9. Perform the same manipulations as on the individual reports, namely:
   1. Sorting the list alphabetically, and highlight key proteins:
      1. For Genetech- "C3 ...", "Clusterin", "Metaloproteinase", "Vitronectin"
      2. For Visual Cyclel "CRALBP, LRAT, RPE65, RDH5, Ezrin, etc...
   2. Sort the list by Number of iTRAQ Peptides, and split off the One-hit wonders into a seperate list following the more reliable identifications
   3. Sort the proteins with 2 or more IDs by iTRAQ ratio with the largest number (ie most abundant in diseased vs Normal) at the top with the rest descending.
10. With the requirements met, Save Worksheet as ("SummaryReport") in the excel report file.
11. When presenting report, It may be necessary to sort the proteins in the report to list only the proteins found in all the samples, so our sort settings are:
    1. Sort By: Frequency
    2. Then by: iTRAQ Ratio.
12. When preparing report address presentation settings including:
    1. Add Title- updated with relevant details- especially Sample number and date
    2. Add header rows with exact labels,
    3. specific Type-size,
    4. font,
    5. Boldness,
    6. Column Width,
    7. Merged,
    8. centered,
    9. number of Significant digits.