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About ABRF sPRG 2007 Protein Study File Upload
ProteomeCommons.org has set up simple web interface for uploading files for the ABRF sPRG 2007 protein identification study. You can use this page to upload your results (even for really big files) in a secure and anonymous fashion. You may also use this page to verify that your files have been successfully uploaded. If you'd like to get started, you need only know your ABRF number and the files that you wish to upload.

ABRF sPRG 2007 File Upload Utility

READ ME FIRST. Before you try to upload anything.

It is critical that you are realistic about uploading data, especially large amounts of data (say a complete LC-MSMS run). If you are on a very fast net connection, expect it to take an hour+ to upload your data. Do not be surprised if it takes more than several hours, possibly overnight to upload your data. It may even take all weekend if you have a slower net connection and you are uploading lots of small files.

The best thing that you can do is to use the Upload Tool and let it run for as long as it takes. Feel free to use your computer as you normally do while the tool is running. If you notice that your computer is sluggish while uploading files, please see the Tranche guide on setting the uploader to a "low priority".

It is OK to restart the upload tool and/or accidentlly upload a file more than once. The file upload tool will skip previously uploaded files and previously uploaded portions of big files. If you cancel half-way through a upload, the tool will automatically resume next time you try to upload the file.

Step-by-step guide to uploading files

You are encouraged but not required to upload your ABRF sPRG 2007 data. Data means in the least your peak lists and spectra annotation information; however, it would be great if you also uploaded files such as your raw spectra, search engine output files, and any other file that is related to the data analysis. ABRF is using Tranche to host data, and plenty of space is available for file uploads. Even really large file uploads.

In order to upload your data, it is suggested that you make one large directory of files. The Upload Tool will ask for your ABRF participant number and a directory to upload. If you select the directory that you've made, that exact directory structure will be uploaded. That is also the directory structure others will see when they download the data.

You do not need to convert your data in to any special format (e.g. mzData or mzXML). Easy to read formats are helpful, but the raw data that comes directly off your mass spec is also valuable. Here is the suggested directory structure to make for your upload.

  1. Make a README.txt file that contains basic information about your experimental details and the files you have uploaded.
  2. Make a directory named "peaklists" to store all of your monoisotopic, centroided peaklists.
  3. Make a directory named "spectra" to store all of your raw spectra.
  4. Make a directory named "search-results" to store all of your de novo and MS/MS search results.
  5. Make a directory named "images" to store all of your annotated peptide identification images.
  6. Include all other files that don't fall in to the above categories in intuitively named directories. Please note these directories in your README.txt file so that others can more easily figure out what files are available.

When you are ready to upload your files click on the Upload Tool link to start the upload. It'll ask for your ABRF participant number and the directory to upload. Click on the "Check/Upload" button to upload the files. A progress bar will appear along with an estimated time to complete the upload. Sit back and wait for the upload to finish -- running uploads overnight is a great idea for larger sets of files. If for any reason the upload is disrupted (e.g. loss of net connection or computer reboot) don't worry. Simply restart the upload tool and it will pick up where it left off.

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