IMP-apQuant

IMP-apQuant is a Proteome Discoverer node for accurate and precise label-free quantification of peptides and proteins.

Downloads for 8 PD versions
PD3.3
IMP-apQuant-Setup.exe 12.2 MB · 2026-02-16 SHA-256 dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
SHA-256dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
MD55d694f895327d9ccf99ba82bd4ce4106

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant-Setup.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | shasum -a 256 -c -
PD3.2
IMP-apQuant-Setup.exe 12.2 MB · 2026-02-16 SHA-256 dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
SHA-256dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
MD55d694f895327d9ccf99ba82bd4ce4106

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant-Setup.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | shasum -a 256 -c -
PD3.1
IMP-apQuant-Setup.exe 12.2 MB · 2026-02-16 SHA-256 dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
SHA-256dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
MD55d694f895327d9ccf99ba82bd4ce4106

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant-Setup.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | shasum -a 256 -c -
PD3.0
IMP-apQuant-Setup.exe 12.2 MB · 2026-02-16 SHA-256 dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
SHA-256dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
MD55d694f895327d9ccf99ba82bd4ce4106

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant-Setup.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | shasum -a 256 -c -
PD2.5
IMP-apQuant-Setup.exe 12.2 MB · 2026-02-16 SHA-256 dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
SHA-256dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
MD55d694f895327d9ccf99ba82bd4ce4106

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant-Setup.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | shasum -a 256 -c -
PD2.4
IMP-apQuant-Setup.exe 12.2 MB · 2026-02-16 SHA-256 dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
SHA-256dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
MD55d694f895327d9ccf99ba82bd4ce4106

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant-Setup.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | shasum -a 256 -c -
PD2.3
IMP-apQuant-Setup.exe 12.2 MB · 2026-02-16 SHA-256 dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
SHA-256dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911
MD55d694f895327d9ccf99ba82bd4ce4106

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant-Setup.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant-Setup.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant-Setup.exe' && echo 'dfdc210be27a65d48efbd714d08c3dc0310cd3b6849096c6f9b2f263e1788911  IMP-apQuant-Setup.exe' | shasum -a 256 -c -
PD2.1
IMP-apQuant_PD_2_1_setup_wo_R.exe 1.6 MB · 2018-11-09 SHA-256 a471b29242e8dd2c0a50b1d87f7d6e3e69a43f4e155300489d95fa1d53be0a88
SHA-256a471b29242e8dd2c0a50b1d87f7d6e3e69a43f4e155300489d95fa1d53be0a88
MD54169aa1bf66cc0d965a16674021933d3

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'IMP-apQuant_PD_2_1_setup_wo_R.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant_PD_2_1_setup_wo_R.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'a471b29242e8dd2c0a50b1d87f7d6e3e69a43f4e155300489d95fa1d53be0a88') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'IMP-apQuant_PD_2_1_setup_wo_R.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant_PD_2_1_setup_wo_R.exe' && echo 'a471b29242e8dd2c0a50b1d87f7d6e3e69a43f4e155300489d95fa1d53be0a88  IMP-apQuant_PD_2_1_setup_wo_R.exe' | sha256sum -c -
curl -fL -o 'IMP-apQuant_PD_2_1_setup_wo_R.exe' 'https://ms.imp.ac.at/data/apQuant/IMP-apQuant_PD_2_1_setup_wo_R.exe' && echo 'a471b29242e8dd2c0a50b1d87f7d6e3e69a43f4e155300489d95fa1d53be0a88  IMP-apQuant_PD_2_1_setup_wo_R.exe' | shasum -a 256 -c -

Not supported: PD1.3, PD1.4, PD2.0, PD2.2.

Features

  • NEWQuantification of Crosslink Areas (Proteome Discoverer 2.3 and up)
  • FDR based quantification confidence
  • 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

Manual

For a small manual on how to install and use apQuant, and what all these confusing parameters mean, refer to this one: Manual.

Proteome Discoverer version

Prerequisites

apQuant requires:

Installation

Prerequisites

apQuant requires:
  • an installation of Proteome Discoverer version 2.3

Installation

Prerequisites

apQuant requires:
  • an installation of Proteome Discoverer version 2.4

Installation

Prerequisites

apQuant requires:
  • an installation of Proteome Discoverer version 2.5 or 3.0-3.3

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:

please dowload these files using right-click - "Save Link as..."

What's new?

Date Version Info
2019-01-28 3.1 included crosslink quantification
2017-12-19 3.0 project renamed to IMP-apQuant
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

Screenshots

Processing workflow

Processing parameters

Consensus workflow

Consensus parameters

Peptides

Proteins

Extracted ion chromatogram of a peptide in six samples.
PSMs are depicted in red, integration boundaries in orange and the peaks center of gravity in blue.