Dear Colleagues,

Once again thank you for the work thus far.

Right now, we have the results as seen in the attachment. We’re still waiting for one more group to report. As we discussed previously, we would now like to analyze the raw data collectively. In this way the reasons for any of the incorrect and missed assignments should be easily found and corrected. We also discussed using Tranche and we are very grateful to Phil Andrews and Jayson Falkner for this. We now request that we go ahead with transferring the data.

Since we wish to assure confidentiality we suggest that any trace within the files that leads back to the lab that generated this data be removed. It may be necessary to do a search and replace. For instance, output files from many software packages will include license numbers. Also, in the creation of excel spreadsheets, please check under File/Properties for information regarding the owner of the license that generated the spreadsheet.

Below are the instructions for the preparation of the data that is to be submitted and requests for details.

Many thanks in advance,

   alex

Instructions for PREPARATION OF DATA for submission to Tranche:

1. Select a name for your data-package (6 to 20 characters – letters or numbers only please).  This name will be known only by you and Alex Bell.  Do not use a name that might identify you or your laboratory.

2. Create the following directory tree on your local computer.

3. Rename “New Folder” to the name you choose for your data package. This is the folder you should upload to Tranche.

4. Please prepare a “methods_file” which should contain a complete accounting for methodologies for each of the following categories

• MS data collection (please ensure that the following are ALSO included: i) time in minutes of all LC separations; ii) for 2D-LC identify first column type (SCX, Wax, other); iii) for MALDI ToF ToF the number of spots and the number of ions fragmented
• Tandem MS data processing (generation of peaklists; also indicate if temperature fluctuations were monitored and if so was a correction made when processing the data)
• Database search analysis (software, parameters, etc)
• Criteria for peptide identification (Mascot ID/homology score, Sequest parameters, other)
• Criteria for protein identification (e.g. 2 peptides above ID score)

5. Complete the attached Word document (HUPO_Test_Sample_reporting_Additional_Info_LIMS). This data is required for the LIMS module of CellMapBase.

6. Place both files described in steps 4 and 5 in the top directory as indicated below:

7. Copy the mass spec files into folder “mass_spec”.

8. Copy the peaklist files into folder “peaklist”.

9. Copy the search engine output files (for the Mascot search engine this is the xxx.dat file) into the “search_resultfile” directory (peptide identifications).

Reminder:  Make sure that there is no information in these files that would identify you, or your lab, or the institution.

10. Copy your file containing your protein identifications into directory “proteinlist”.  This list was generated by the search engine or your summarizing software from the search results.

11. Copy the Excel file containing your FINAL protein summary list into directory “proteinlist”.  This final summary list (with peptide statistics) was generated after interaction with Alex Bell.

SUBMISSION TO TRANCHE

The data is to be uploaded to Tranche at

http://tranche.proteomecommons.org/examples/hupo-2007/Tranche-HUPO.jsp

At this site, you will need to enter an email address (required to retrieve your unique identifier).  After clicking on “upload data”, you will be prompted to identify/select the folder (created above – steps 1-11) that is to be uploaded.

This web-interface will direct your submission to the HUPO-2007 project at Tranche.  Subsequent to your submission, you will be issued 1 Tranche hash that uniquely identifies your data.  Please communicate the Tranche hash to Alex Bell (alex.bell@mcgill.ca).