Skip to content
DART-ID: retention time alignment and peptide identification confidence updates
Python C HTML Other
Branch: master
Clone or download
Nikolai Slavov Nikolai Slavov
Nikolai Slavov and Nikolai Slavov Update
Latest commit 4395fc5 Jul 21, 2019
Type Name Latest commit message Commit time
Failed to load latest commit information.
config_files move filters to the front in example config files May 24, 2019
dart_id bump version May 28, 2019
docs Update Jul 21, 2019
example example configuration file for sequest data May 24, 2019
.gitignore ignore testing/development scripts May 17, 2019
LICENSE.txt update license Feb 16, 2019 validate configuration file with jsonschema May 22, 2019 add more install instructions May 28, 2019 update flags Jan 18, 2019
environment.yml validate configuration file with jsonschema May 22, 2019
requirements.txt fix conda environment creation Mar 23, 2019
setup.cfg validate configuration file with jsonschema May 22, 2019


GitHub release PyPI PyPI - Downloads GitHub



Getting started


DART-ID requires Python >= 3.4 (64-bit - miniconda distribution recommended), and has been tested on Windows 8 / OSX Mojave 10.14 / Centos 7 / Ubuntu 14.04.


DART-ID is available on PyPI and can be installed with pip.

pip install dart-id


DART-ID requires a YAML-formatted configuration file to run. An example annotated config file can be found in example/config_annotated.yaml. You can specify input files and the output folder on the command line, if that's what you prefer.

View the command-line arguments anytime by running: dart_id -h.

usage: dart_id [-h] [-i INPUT [INPUT ...]] [-o OUTPUT] [-v] [--version] -c

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT [INPUT ...], --input INPUT [INPUT ...]
                        Input file(s) from search engine output (e.g.,
                        MaxQuant evidence.txt). Not required if input files
                        are specified in the config file
  -o OUTPUT, --output OUTPUT
                        Path to output folder
  -v, --verbose
  --version             Display the program's version
  -c CONFIG_FILE, --config-file CONFIG_FILE
                        Path to config file (required). See

Example runs

An example configuration file can be downloaded from GitHub:

The first few lines of the above configuration file specify the path to the input file:

## Input
## ==========================

  - /path/to/SQC_67_95_Varied/evidence.txt

You can download the evidence.txt file from MassIVE:

Then edit the path to the file downloaded, and run the following command:

dart_id -c config_files/example_sqc_67_95_varied.yaml -o ~/DART_ID/SQC_67_95_varied_20181206

The -o parameter points to the output folder for DART-ID. You can also specify this path in the config file.

An example analysis of the data and configuration file specified above is available publicly at

About the project

DART-ID is a project developed in the Slavov Laboratory at Northeastern University Bioengineering, and was authored by Albert Tian Chen, Alexander Franks (of UCSB Statistics and Applied Probability), and Nikolai Slavov.

The manuscript for this tool is available on bioRxiv:

Contact the authors by email: nslavov{at}


DART-ID is distributed by an MIT license.


Please feel free to contribute to this project by opening an issue or pull request in the GitHub repository.


All data used for the manuscript is available on UCSD's MassIVE Repository


Scripts for the figures in the DART-ID manuscript are available in a separate GitHub repository,

You can’t perform that action at this time.