How to Convert Your Data to Limelight XML
Limelight is designed to support data generated by any mass spec data processing pipeline. To accomplish this, we have designed a file format called Limelight XML that implements an XML schema that stores the data that Limelight needs in the most generalized way possible. Data that are uploaded to Limelight need to be formatted as Limelight XML. And, importantly, any data represented as Limelight XML can be uploaded to Limelight–regardless of the software pipeline that generated the data.
What are Converters
Converters are programs that convert the native output of software pipelines to Limelight XML that can be imported into Limelight.
This design moves the job of reading the output of different software pipelines to smaller individual programs we call converters. Each of these programs can be maintained individually, separate from Limelight–ensuring they stay current. And adding support for a new search pipeline becomes the relatively simple matter of writing a converter for the output of that program.
How to Get Converters
We have written a number of converters for popular mass spec processing pipelines. Follow the links below to the GitHub repository for the individual converter for information on how to run that converter.
Comet + Percolator |
https://github.com/yeastrc/limelight-import-comet-percolator |
Comet + Trans Proteomic Pipeline |
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Comet-PTM |
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Crux |
https://github.com/yeastrc/limelight-import-crux-comet-percolator |
Magnum + Percolator |
https://github.com/yeastrc/limelight-import-magnum-percolator |
Magnum + Trans Proteomic Pipeline |
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MetaMorpheus |
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modA |
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MSFragger |
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MSFragger + Trans Proteomic Pipeline |
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Open pFind |
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Philosopher (MSFragger or Comet) |
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ProLuCID (processed with DTASelect, using IP2) |
https://github.com/yeastrc/limelight-import-prolucid-dtaselect |
Tag Graph |
How to Run Converters
Each of the above converters has a link to the specific converter’s GitHub repository with instructions for running that specific converter. Each converter has slightly different options related to the specific pipeline being converted.
In general, the process of converting your data to Limelight XML would work like the following:
Run your pipeline and generate your results.
If not already installed, download the converter program from one of the above repositories.
Follow the directions for running the converter. Generally each converter will require that you specify the following by passing it command line parameters when you run the program:
The data file(s) generated by the search pipeline
The configuration file used to run the search
The FASTA file containing the sequences searched
Now the resulting Limelight XML may be uploaded to Limelight.
Getting Help or Requesting a New Converter
If you have any questions, bug reports, or requests for new converters, please contact us!
Try using the Limelight Issue Page at GitHub.
You can join our Slack and chat with us.
You can email us at limelightms@uw.edu