Binner for Reduction of MS Data

When a metabolite is analyzed by electrospray ionization-mass spectrometry (ESI-MS), it is usually detected as multiple ion species due to the presence of isotopologues, adducts, and in-source fragments that cannot be readily identified. Binner is a Java application that takes a numerical feature table obtained from any preprocessing software (e.g. XCMS, MZmine) as input and outputs a file with clusters of closely eluting, highly correlated metabolite features that are most related, along with their pairwise correlations, mass differences, and putative annotations.


Executable Release Date Description
binner-1.0.0.jar 08/02/19 First public release
binner-0.9.15.jar 12/21/18 First external release

Note: When downloading to a Mac, depending on your security settings, you may get an "unidentified developer" message when first attempting to launch the program. If this occurs, please navigate to System Preferences -> Security & Privacy and click on the "Open Anyway" button in order to allow the program to launch.

Input Files

(Right Click... Save Link As... to download)

Binner's primary input is an aligned feature table. This intensity data should be in tsv (.txt) file format and contain the following mandatory columns for each feature :

  1. A unique compound (feature) identifier
  2. Mass-to-charge ratio (m/z)
  3. Retention time
  4. Feature intensities for individual samples

A Binner annotation file specifies information for each charge carrier, neutral loss or adduct you'd like Binner to consider when annotating features. It contains five mandatory columns :

  1. Annotation
  2. Mass
  3. Mode
  4. Charge
  5. Tier

For a detailed description of the Binner annotation algorithm, please refer to the Binner user manual.

Cite Binner

Maureen Kachman, Hani Habra, William Duren, Janis Wigginton, Peter Sajjakulnukit, George Michailidis, Charles Burant, Alla Karnovsky.
Deep annotation of untargeted LC-MS metabolomics data with Binner.
Bioinformatics, btz798, 23 October 2019