PEAKS: ABI 4700/4800

The 4700 and 4800 ABI instruments use an Oracle database to store the MS spectra. Extracting the data and packaging it into a readable file format is required to use the PEAKS software.

Extraction of the data for PEAKS requires our homegrown software that we call simply “ABI 4700 Data Extractor”. The resulting data type is a .pkl file that PEAKS call read directly. The “ABI 4700/4800 Data Extractor” need not be on the same system as the Oracle database, but the location and excepting port number of the server will need to be known. The login and password is also passed to the Oracle database server with this software. Have all this information when you are using the extractor.

The tool can be downloaded from: http://www.bioinformaticssolutions.com/downloads/abi . This username and password can be provided by your BSI Sales Rep.

Double click on "ABI.exe" and save the software to a location that can be easily found. Double click the “ABI4700DataExtractor.exe” setup icon. The first window that will require input will be the “Introduction”. Follow the install instructions and have some idea where you would like to install the software. The default location is “C:\Program Files\BSI Software”. Continue to follow the instructions of the installation program. When you have finished the installation, go to the location where the extractor was installed and double click the “ABI 4700 Data Extractor” icon. (The 4700 Extractor software works for both 4700 and 4800 instruments).

The window below will appear. Select “File”, “Settings” and the “ABI Data Server Configuration” pop-up window will appear (as seen directly below). The default settings for the tool will appear. These settings must be changed to the Oracle Server’s settings (server’s name or IP address and port access) with a valid User ID and Password. Click the “Configure” button to change the settings.

Contact the network manager or IT department for this information. After the correct information has been entered, click “Next”. The window below will appear. Click the “Test” button and the software will attempt to connect with the Oracle server. When a connection has been made with the server, select “File”, “Load Spot Set List from the Database”. The software will load the Spot Set List and the “Open Spot Set” option will become available. Select “File” and “Open Spot Set”, select a spot set and click “OK” to open it. The “Job Run” information for the spot set. Each “Job Run” will have its own radio button. Select the “MS/MS” job. This will provide the precursor information. Click the “Convert” button to perform the data extraction. A “Save As” window will appear to save the extracted data. Provide a file name and a location for the data.

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De Novo Sequencing Protein ID inChorus PTM Seq. Tag Search Raw Data Download Demo Request Prices Tech Support Our Research User Comments	Superior de novo sequencing and protein ID Software PEAKS Extracting ABI 4700/4800 data from your Oracle database The 4700 and 4800 ABI instruments use an Oracle database to store the MS spectra. Extracting the data and packaging it into a readable file format is required to use the PEAKS software. ABI 4700/4800 Data Extractor from BSI Extraction of the data for PEAKS requires our homegrown software that we call simply “ABI 4700 Data Extractor”. The resulting data type is a .pkl file that PEAKS call read directly. The “ABI 4700/4800 Data Extractor” need not be on the same system as the Oracle database, but the location and excepting port number of the server will need to be known. The login and password is also passed to the Oracle database server with this software. Have all this information when you are using the extractor. The tool can be downloaded from: http://www.bioinformaticssolutions.com/downloads/abi . This username and password can be provided by your BSI Sales Rep. Double click on "ABI.exe" and save the software to a location that can be easily found. Double click the “ABI4700DataExtractor.exe” setup icon. The first window that will require input will be the “Introduction”. Follow the install instructions and have some idea where you would like to install the software. The default location is “C:\Program Files\BSI Software”. Continue to follow the instructions of the installation program. When you have finished the installation, go to the location where the extractor was installed and double click the “ABI 4700 Data Extractor” icon. (The 4700 Extractor software works for both 4700 and 4800 instruments). The window below will appear. Select “File”, “Settings” and the “ABI Data Server Configuration” pop-up window will appear (as seen directly below). The default settings for the tool will appear. These settings must be changed to the Oracle Server’s settings (server’s name or IP address and port access) with a valid User ID and Password. Click the “Configure” button to change the settings. Contact the network manager or IT department for this information. After the correct information has been entered, click “Next”. The window below will appear. Click the “Test” button and the software will attempt to connect with the Oracle server. When a connection has been made with the server, select “File”, “Load Spot Set List from the Database”. The software will load the Spot Set List and the “Open Spot Set” option will become available. Select “File” and “Open Spot Set”, select a spot set and click “OK” to open it. The “Job Run” information for the spot set. Each “Job Run” will have its own radio button. Select the “MS/MS” job. This will provide the precursor information. Click the “Convert” button to perform the data extraction. A “Save As” window will appear to save the extracted data. Provide a file name and a location for the data. If any errors or inaccuracies are noted from this page please contact us.