ProSightPD™

See the trees for the forest with the most powerful proteoform search engine at your fingertips.

 See more with ProSightPD.

Analyze top-down proteomics data with speed, accuracy, and precision using our ProSight search engine.

Explore top-down data.

Easily navigate fully-integrated top-down data inside the Proteome Discoverer environment. Explore different levels of data— from proteins to MS/MS spectrum info— and seamlessly move across them.

Experience full proteoform quantitation.

Perform label-free proteoform quantitation. A wide range of intuitive visualization tools are at your disposal to help you assess results and discover new targets. Interactive plots allow you to quickly identify evidence-backed proteoforms of interest.

Get an in-depth view of the data behind your proteoforms.

Visualize spectral data in detail for each proteoform found by ProSight, from precursor to fragment ions. View individual quant traces and feature groups from quantitation results.

Open search results seamlessly in external tools.

Deep dive into proteoform fragmentation matches with ProSight Lite and TDValidator. Browse protein identification and FDR results with TDViewer.

Curate, create, and customize databases.

Curate top-down databases with Database Manager. Create and customize UniProt™-formatted XML files using ProSight Annotator’s intuitive user interface. Protein sequences can be easily added, removed, or edit with post-translational modifications and other features of interest.

Features

Analyze.

  • Put ProSight’s versatility to use on any type of Thermo mass spectrometry fragmentation technique, including UVPD, EThcD, HCD, CID, SID, and ETD.

  • Process both PTCR and FAIMS data.

  • Determine masses for large and small proteins.

Search.

  • Search top-down proteomics data with the powerful ProSight search engine.

  • Look for truncations and cleavage products with subsequence search.

  • Calculate false-discovery rate.

  • Modify protein databases with ease using ProSight Annotator.

Process.

  • Analyze at blazing speeds with parallel processing.

  • Search the known modification space at ultra-fast speeds with ProSight’s unique Uniprot-derived databases.

  • Match fragment ions for single proteoforms from direct infusion data.

Quantitate

  • Deploy sliding window deconvolution to quantitate mass species.

  • Link results to proteoform identifications.

  • Perform label-free quantitation at the proteoform level. 

  • Get full access to Proteome Discoverer’s statistics platform.

Visualize.

  • Open search results seamlessly in TDValidator, ProSight Lite, and TDViewer.

  • Browse protein identification and FDR results with TDViewer.

  • Deep dive into proteoform fragmentation matches with ProSight Lite and TDValidator.

Detect.

  • Determine intact protein masses and fragment ion masses from isotopic distributions using the Xtract algorithm.

  • Deconvolute higher mass, unresolved proteoforms with the kDecon charge state mass determination algorithm.

See what’s possible with ProSightPD.

ProSightPD can be used in a wide range of applications across diverse research fields.

Modification Identification

Search modifications with confidence. By using annotated modifications from UniProt™ or custom XML files, ProSightPD assigns only modifications with empirical evidence for their existence. Unknown mass shifts can also be used to account for mass differences and to assign additional fragmentation ions.

Cleavage/Truncation Identification

Look for endogenous cleavages and protein truncations. Cleavage sites can be determined on the N-terminus, C-terminus, or both termini.

Label-Free Quantitation

Quantitate differences in proteoform abundances across label-free sample types using the Proteome Discoverer™ statistical engine. Sliding window deconvolution with kDecon and Xtract unlocks robust quantitation for proteoform masses, large and small.

Antibody Identification

Search large mass data such as antibody subunits and intact antibodies using the high mass capabilities of ProSightPD. The kDecon algorithm can determine masses from large proteoforms with unresolved charge state distributions, which can narrow the search range. Integration with ProSight Annotator allows custom sequences and modifications to be annotated and searched.

See ProSightPD in the wild.

ProSight has been used by hundreds of labs all around the world. Get inspired by the cutting-edge researchers who have used ProSightPD to accelerate their discoveries.

Dissecting Ribosomal Particles Throughout the Kingdoms of Life Using Advanced Hybrid Mass Spectrometry Methods

Nature Communications

Michiel van de Waterbeemd, Sem Tamara, Kyle L. Fort, Eugen Damoc, Vojtech Franc, Philipp Bieri, Martin Itten, Alexander Makarov, Nenad Ban & Albert J. R. Heck

Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination

Journal of Proteome Research

Mathieu Dupré, Magalie Duchateau, Christian Malosse, Diogo Borges-Lima, Valeria Calvaresi, Isabelle Podglajen, Dominique Clermont, Martial Rey, and Julia Chamot-Rooke*

Capillary Zone Electrophoresis-Tandem Mass Spectrometry as an Alternative to Liquid Chromatography-Tandem Mass Spectrometry for Top-down Proteomics of Histone

Analytical Chemistry

Daoyang Chen, Zhichang Yang, Xiaojing Shen, and Liangliang Sun.

See faster with ProSightPD.

Whatever the destination, get there faster with our workflows, tutorials, and personalized expert support.

Guides & Tutorials

Find information you need to fuel your proteome exploration. We offer an extensive user guide for ProSightPD to jumpstart your journey and are currently developing more resources to help you fine-tune your search. (Tutorials coming soon.)

Workflow & Analysis Templates

Get a head start with fit-for-purpose templates that simplify creating a workflow. Find processing workflow templates, consensus workflow templates, and analysis templates, which have all been tested and optimized for confident proteome analysis.

Expert Support

Get personalized help with one of our experts. Ask questions over email or set up a virtual consultation to discuss your research goals and workflow, better understand our products, or troubleshoot. No project is too big or small.

See for yourself.

ProSightPD nodes are fully integrated into the Thermo™ Proteome Discoverer™ software framework. We offer a range of licensing options for ProSightPD to give top-down researchers greater flexibility in customizing their analytical toolkits.

Great for TD-Only Researchers

ProSightPD in Proteome Discoverer VIEWER

Get ProSightPD 4.3 in Proteome Discoverer VIEWER 3.1. Previous versions of ProSightPD (4.1 and earlier) have required a license for Proteome Discoverer in order to use ProSightPD. With the new standalone release (4.3), ProSightPD users will no longer need to purchase a separate Proteome Discoverer license, providing a more affordable option for top-down only researchers. While Proteome Discoverer VIEWER will have all the features of Proteome Discoverer BASE, bottom-up search engines SEQUEST™ HT and Mascot will not be available.

Upgrade from older ProSightPD/ProSightPC

Upgrade from older ProSightPD (4.1 or earlier) or ProSightPC licenses to standalone ProSightPD 4.3 in Proteome Discoverer VIEWER 3.0 for a reduced price. See previous option for details.

Great for TD-Flexible Researchers

ProSightPD in Proteome Discoverer BASE

Get ProSightPD 4.3 in Proteome Discoverer BASE 3.1, which includes bottom-up search engines SEQUEST™ HT and Mascot. Both Proteome Discoverer BASE and the standalone ProSightPD are available for demo.

ProSightPD with Third Party node suite in Proteome Discoverer BASE

Get ProSightPD 4.3 as a part of the Third Party nodes suite in Proteome Discoverer BASE 3.0. Permanent license for ProSightPD 4.3 can be purchased separately. Both Proteome Discoverer BASE and the 3rd-party nodes are available for demo.

Test Drive ProSightPD

Select instructions below for accessing your free demo.

  • Clicking Free Demo will bring you to the Life Sciences Mass Spectrometry Software Download and Licensing Portal. If you do not already have a portal account, you can register here.

    After log in, find the installer page for both ProSightPD 4.3 and Proteome Discoverer 3.1 as follows:

    1. Click on Software & Services > Product List in the left menu.

    2. Select Application - ProSightPD.

    3. Find the installer page for Thermo ProSightPD 4.3 and select the Thermo ProSightPD 4.3.exe installer (includes Proteome Discoverer VIEWER, unlicensed version).

    BASE refers to the licensed version of Proteome Discoverer, while VIEWER refers to the unlicensed version. You will not see this naming in the installers.

  • Clicking Free Demo will bring you to the Life Sciences Mass Spectrometry Software Download and Licensing Portal. If you do not already have a portal account, you can register here.

    You will need to first install Proteome Discoverer 3.1 BASE:

    1. After log in, click on Software & Services > Product List

    2. Select Application - Proteome Discoverer.

    3. Find the installer page for Proteome Discoverer 3.1.

    Then find the installer page for both ProSightPD 4.3 as follows:

    1. Click on Software & Services > Product List in the left menu.

    2. Select Application - ProSightPD.

    3. Find the installer page for Thermo ProSightPD 4.3 and select the Thermo ProSightPD 4.3.exe installer (includes Proteome Discoverer VIEWER, unlicensed version). You can skip the Proteome Discoverer VIEWER installation step.

    BASE refers to the licensed version of Proteome Discoverer, while VIEWER refers to the unlicensed version. You will not see this naming in the installers.

  • Clicking Free Demo will bring you to the Life Sciences Mass Spectrometry Software Download and Licensing Portal. If you do not already have a portal account, you can register here.

    You will need to first install Proteome Discoverer™ BASE from the Proteome Discoverer installer page followed by the Third Party nodes:

    You will need to first install Proteome Discoverer 3.1 BASE:

    1. After log in, click on Software & Services > Product List

    2. Select Application - Proteome Discoverer.

    3. Find the installer page for Proteome Discoverer 3.1.

    4. Find the installer page for the Thermo Proteome Discoverer ThirdParty 3.1.

    BASE refers to the licensed version of Proteome Discoverer, while VIEWER refers to the unlicensed version. You will not see this naming in the installers.

Request Quote

To purchase, contact your Thermo Sales Rep directly for a quote. If a rep isn’t available to you, please contact us for more info.

Frequently asked questions.

  • ProSightPD 4.2 is compatible only with Proteome Discoverer 3.0 BASE and Proteome Discoverer v. 3.0 VIEWER. Multiple versions Proteome Discoverer software can be installed on the same computer.

  • Yes. The installer for the standalone ProSightPD is different from the 3rd-party nodes installer, both of which can be found in the Thermo Scientific™ Life Sciences Mass Spectrometry Software Download and Licensing Portal. Follow the instructions under Try ProSightPD (Free Demo) to find the right installer.

  • Free 60-day demos are automatic and begin after installation. To purchase a permanent license, contact your Thermo Sales Representative for a quote. 

  • Your computer must meet the minimum technical specifications outlined below to run and use ProSightPD.

    Applicable for April 2022 release (version 4.2) and later:

    • Proteome Discoverer 3.0 VIEWER or BASE.

    • Microsoft™ Windows 10 with latest service pack.

    • For more details see the Release Notes.

Photos by Kal Visuals; Ali Kazal; Christin Hume on Unsplash.