Out now – Progenesis QI for proteomics v4.1

We are pleased to announce that a new version of Progenesis QI for proteomics has been developed which is now available to download.

What’s New in this v4.1 release?

Improved Spectral libraries: adding to database search flexibility

Improved spectral library searching generates huge time savings so you can quickly focus your efforts on new and interesting features.

Progenesis QI for proteomics v4.1In Progenesis QI for proteomics v4.1 you can:

  • Build up a library of verified identifications from DDA, MSE, HDMSE and SONAR data including:
    • Fragmentation patterns seen in your own experiments and with your own instrumentation
    • Retention time information
    • Highlight overlapping ions to show potential interferences
    • You can also collaborate internally and externally by sharing these libraries with collaborators. This avoids duplication of effort within the Progenesis community.
  • Search the library first in a new discovery experiment
    • Quickly find peptides that match something you’ve seen before
    • Hide strong spectral library matches
    • Submit the remaining unknowns for traditional search methods
    • Supports NIST and Mascot .msp files and SWATH Atlas .sptxt files
  • Append any new verified identifications to the library

MS/MS Spectral clean-up tools during library creation

A new tool in the “Resolve conflicts” section indicates the identified peptides that have co-eluting peptides in close proximity.  This gives the user the option to exclude the MS/MS spectra of these peptide ions from the spectral library export, thereby only exporting peptides which should give cleaner matching in future identifications.

Only identified fragments from the MS/MS spectra are included when you create a library, ensuring the MS/MS data used in the spectral library are as “clean” as possible.


A reminder of what’s new in v4.0…


Support for SILAC: Progenesis QI for proteomics now seamlessly integrates with Proteolabels software, with workflows for SILAC and dimethyl labelling.


Integration with Symphony: you can now create a Progenesis QI for proteomics experiment from the Symphony data pipeline.



Support for SONAR data: SONAR is the latest DIA mode from Waters, providing additional specificity and clarity.


Export to PRIDE: mzIdentML exports can now be produced for upload to the PRIDE repository.

Other improvements

  • Improved workflow for Waters MSe data, with automatic peak detection thresholding to maximise number and quality of identifications, whilst improving software performance.

For more details, please download our “What’s New” document.

Where can I download it?

If you’re an existing customer with an up to date support plan, this upgrade is totally free of charge and very simple – click on the upgrade in the software panel. In addition, if your Progenesis PC is connected to the internet, there should be a message in the experiments list sidebar notifying you of this new version – if you click this, and your dongle is plugged in, you’ll be sent to the download page.

If you are out of your support period, please contact us and we can discuss getting you back in support.

If you’re thinking of trying Progenesis QI for proteomics for the first time, you can download the software from here.

How will I know how to get the most out of the new features?

We’ve expanded our FAQs to cover the new features, as well as updating any previously available FAQs to reflect new behaviour. We’ve also updated our user guide if you’re looking for a step-by-step guide from start to finish.