IMP-apQuant is a Proteome Discoverer node for label-free quantification of peptides and proteins. It is also formerly known as Peakjuggler
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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.
|2017-05-30||3.0||feature based scoring of quantification confidence,
|2016-11-09||2.18||RAM and time usage reduced,
|2016-06-16||2.14||RAM usage decreased,
separate installer for PD 2.0
|2016-06-02||2.13||several small bug fixes|
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.