IMP-apQuant

IMP-apQuant is a Proteome Discoverer node for label-free quantification of peptides and proteins. It is also formerly known as Peakjuggler

Features

  • NEW FDR based quantification confidence
  • NEW Machine-learning based scoring algorithm
  • Retention time alignment
  • Visualisation of extracted ion chromatograms and integration boundaries
  • Peptide identity propagation ("match between runs")
  • Support of razor peptides, TopN and iBAQ

Prequisites

  • An installation of Proteome Discoverer version 2.1
  • An installation of R

Installation

Sample Workflow

This sample workflow should make you ready to go. It is the workflow to analyse the Ramus et al data set which is also used in the performance comparison further down in the Performance section.

Support

We have a forum. Feel free to ask questions and give feedback!

Performance

We benchmarked IMP-apQuant on a publicly available dataset (Ramus et al). The original raw files are available on PRIDE (PXD001819). The samples are comprised of UPS1 protein mix spiked in at different concentrations into a 1:1 yeast background. This dataset was used in a comparison for different LFQ algorithms (Veit et al). We used results published there as Supplementary Data in order to compare the performance of IMP-apQuant to LFQProfiler(OpenMS), MaxQuant, MFPaQ and Skyline.

IMP-apQuant outperforms these tools by enabling the detection of more differentially abundant UPS proteins at the same number of falsely identified (unregulated) yeast proteins.

The Proteome Discoverer workflow to reproduce this result is available for download and provides a starting point for easy incorporation of IMP-apQuant in your workflow. Furthermore the final results file is also available here.

Downloads:

What's new?

Date Version Info
2017-05-30 3.0 feature based scoring of quantification confidence,
iBAQ support
2016-11-09 2.18 RAM and time usage reduced,
stability fixes
2016-07-25 2.15 scoring finalized,
stability fixes
2016-06-16 2.14 RAM usage decreased,
separate installer for PD 2.0
2016-06-02 2.13 several small bug fixes
2015-05-25 initial release

Manual

Screenshots

Processing workflow

Processing parameters

Consensus workflow

Consensus parameters

Peptides

Proteins

Extracted ion chromatogram a peptide in two samples.
Integration boundaries are shown in orange and the peaks center of gravity is shown in blue.

Other Sample Data

To get you started, we provide you with a sample workflow and also the raw and result files. The sample consists of 0.1 µg Hela measured on a QExHF.

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