Mage
The Mage suite of tools provide access to DMS files and metadata.
Mage Extractor
Mage Extractor can extract MS/MS search results from MS-GF+, X!Tandem, Inspect, or SEQUEST analysis jobs and combine the results into a single tab-delimited text file or a single SQLite database.
To use Mage Extractor, first use one of the top tabs to search for
a series of analysis jobs. For example, you could search for
Datasets that contain qc_shew_2d_11_01_frac and were searched
with analysis tool "tandem".
Next, change "Result Type to Extract" to the appropriate mode given the analysis jobs you searched for. Next define a destination file (or SQLite database). Next, choose the desired filters and/or MSGF cutoff, then click either "Extract Results From Selected Jobs" or "Extract Results From All Jobs"
Results will be read from the specified jobs, filtered, and combined into a single, tab-delimited output file.
Illustrated Example
The following graphic illustrates the steps required to use the Flex Query tab of Mage Extractor to select a series of analysis jobs and obtain the data
- Define filters and click "Get Jobs"
- Define the destination directory and file
- Choose the file type to process
- Choose a filter set (optional) or MSGF cutoff (optional)
- Click the desired "Extract Results" button
Mage File Processor
Mage File Processor can be used to copy files from a series of analysis job or dataset directories to your local computer. The program can either copy each file individually, or it can combine a series of files into a single file.
An alternative mode of operation is to search a local directory on your computer to find matching files, then either copy those files to a new directory, or process those files to combine the data into a single file.
When combining MS-GF+, X!Tandem, or SEQUEST result files together, you can optionally filter the data using one of the standard DMS Filter Sets. Another useful feature is to automatically add the Job column as the first column in each row of data in the combined file.
Illustrated Example
The following graphic illustrates the steps required to use the Flex Query tab of Mage File Processor to select a series of analysis jobs and obtain the associated _isos.csv files
- Define filters and click "Get Jobs"
- Define the filename filter, for example: *_Isos.csv
- Customize the search options
- Whether or not to search subdirectories
- Search for files, directories, or both (typically search for files)
- Whether to use RegEx matching or "File Search" matching
- Note that "File Search" matching supports an asterisk as a wildcard symbol: *
- Define the destination directory
- Optionally apply a prefix to each file, for example the Job number
Mage Metadata Processor
Queries DMS to lookup metadata or stats on the specified datasets.
Ranger
Iterates through a range of values to create all possible combinations of the values.
Contacts
Written by Gary Kiebel and Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics
License
Mage is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause