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.

Table of Current Converters

Comet + Percolator

Comet + Trans Proteomic Pipeline



Magnum + Percolator

Magnum + Trans Proteomic Pipeline




MSFragger + Trans Proteomic Pipeline

Open pFind

Philosopher (MSFragger or Comet)

ProLuCID (processed with DTASelect, using IP2)

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!