Polly™ QuantFit Thermo Scientific™ Compound Discoverer™ Integration
Product & Engineering

Polly™ QuantFit Thermo Scientific™ Compound Discoverer™ Integration

Vipul Jain
March 22, 2020

From peaks to absolute concentrations within minutes for 100s of metabolites

About Polly™ QuantFit

Polly™ QuantFit is a calibration tool used for the absolute quantification of metabolites. For the calculation of absolute concentration, the experiment is done with some standard samples of known concentrations.

Polly QuantFit workflow

1. Intensities are detected in El-MAVEN across all metabolites for all samples

2. This workflow can further be customized as per experimental designs to perform normalization

3. Get mathematical mappings from intensities to concentrations for the standard samples, which are used to calculate concentrations of experimental intensities in Polly™ QuantFit

4. Generate customized visualizations with Ipythons or a concentration plot used for downstream processing

Polly QuantFit UI
Polly™ QuantFit UI

Polly™ QuantFit Features

Metadata Creation: This interface detects the standard samples using a machine learning model and then allows adding concentration across all metabolites in a click

Absolute Quantification: Takes the intensity and concentration values for the standard samples and determines the concentration of the biosamples

Reproducibility and Collaboration: Restore your analysis to the exact state of analysis on QuantFit in one click and share that analysis and reports with collaborators

Normalization w.r.t Internal Standard: Concentrations of biosamples are divided by the concentration of the internal standard, to normalize all metabolites

Scaling: Calculated concentrations can be scaled by any factor to neutralize dilution

Custom Visualization: QuantFit shows the biosample concentration plot across all samples as a bar plot. Further, the iPython interface can be used to view custom plots as per defined cohorts

About Thermo Scientific™ Compound Discoverer™

Thermo Scientific™ Compound Discoverer™ software streamlines compound identification determines real differences between samples and elucidates biological pathways with integrated, powerful software workflows to drive rapid insights from your valuable data.


Polly™ QuantFit Thermo Scientific™ Compound Discoverer™ Integration
Download Node

The node is available for download now.

To guide you through the integration workflow, detailed documentation has been prepared and can be accessed here.

The node created in Thermo Scientific™ Compound Discoverer™ has 3 integrations:

1. MSConvert: It converts .raw data obtained from a mass spectrometer to El-MAVEN accepted formats like .mzML or .mzXML

2. El-MAVEN: For high-quality peak integration in a click using a machine learning model. For better peak integration some parameters have been defined in CD.

3. Polly™ QuantFit: For absolute quantification of the data. This application is hosted on the cloud on Polly™ for processing your data


1. Poster: Determining Pharmacokinetics of Cysteamine with Polly™ QuantFit in collaboration with Shawn Davidson at Princeton University presented at ASMS 2019

2. Poster: Rapid automated absolute quantification of metabolites using Polly™ QuantFit to understand tumor nutrient availability in collaboration with Matt Vander Heiden Lab at MIT presented at ASMS 2019

3. Quant-inar: A webinar on the Polly™ QuantFit Workflow to go from peaks to absolute concentrations within minutes for 100s

Free Demo

You can now try this integration for free. We offer a free demo on our platform. Drop a message to pollydemos@elucidata.io today with your requirements and use case. Alternatively, you can directly book a suitable time here and talk to us.

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