October Newsletter
We are thrilled to share with you our inaugural newsletter!
In this newsletter, we aim to keep you informed and engaged with the latest updates, insights, and developments in our project. Each edition will feature exclusive content, including behind-the-scenes glimpses of our progress, interviews with team members, and expert tips on maximizing the benefits of our software. We believe that your feedback is invaluable, and we encourage you to share your thoughts and suggestions with us. Together, we can create a product that truly meets your needs and exceeds your expectations.
Thank you for being a part of our community. Be sure to follow Proteinaceous and the newsletter on LinkedIn! We look forward to sharing this adventure with you and are excited about what the future holds!
Upcoming Events
Come visit us at HUPO 2025! We will have a poster highlighting new software and would love to hear your insights! Poster #880: Proteoform Studio – A Comprehensive Tool for Automated Intact Protein Acquisition and Analysis on Tuesday, November 11th, 2025. Please reach out to Jacob McCabe if you will be attending!
Join us at HUPO in November to learn more about our intact mass analysis and top-down proteomics software!
ProSight Native Major Changes
Expanding Vendor Support - Bruker Data Files Now Fully Supported
Added support for Bruker data files natively without having to convert to mzML. Currently supported Bruker file types are: Bruker .TSF, Bruker .TDF, and Bruker .BAF. Please let us know if you run into any issues with Bruker data files.
Peptide Mapping Preview
We are integrating our powerful ProSight search engine to manage peptide mapping experiments. This includes batch deconvolution for rapid peptide quantitation, utilizing a FASTA input and a variable PTM search, with support for any fragmentation type. The process is remarkably fast, taking approximately 15 seconds per data file. We are eager to receive feedback on this feature.
Improved kDecon Charge State Deconvolution
The new and enhanced kDecon algorithm has been introduced, thanks to the extensive work by Ken Durbin! Users can opt to use the previous kDecon version in Interactive Decon by deselecting the "Use latest kDecon" option under deconvolution settings. Batch Deconvolution workflows will automatically use the latest kDecon algorithm. We have also updated the way our deconvolved spectra are shown and they now provide a more comprehensive display of spectral noise.
New Intact Mass Spectrum Display in ProSight Native. Intact mass analysis of Trastuzumab showing both the m/z and our newly developed deconvoluted mass spectra.
UV Chromatograms Preview
We have added the capability to quantify mass components based on the UV trace instead of mass deconvolution results or SICs. This feature uses the start and end retention times from deconvolution, along with a "time delay" setting, to calculate AUC values. It is also available in Interactive Deconvolution as a chromatogram option under "Trace". Currently implemented for Thermo files, please let us know if there are other file types you would like us to support.
Batch Deconvolution Mass Components Tab
Based on user feedback, we have restructured the old Overview, Mass Components, and Data File Components tabs to enhance navigation within the results sections. The "Mass Components" tab now includes buttons at the top for navigating masses by viewing single consensus masses, multiple consensus masses with data file filters, or individual data file masses before any merging is performed. Consensus mass buttons appear only when mass consensus merging has been executed. They remain hidden during High-Throughput Screening, when Mass Consensus is disabled (under Settings → Mass Merging), or when processing a single data file.
New Database Manager for Top-Down Search and Targeted Top-Down
We now support ProSight Database (psdb) files, which are centrally stored across all applications. Access the database in several locations: With the ProSight Annotator workflow in the Utilities section of the Homepage, from the Top-Down Search workflow → Search Settings, and in the Targeted Top-Down workflow → Add from databases.
Previewing New Spectral Match Scores
New scores for each fragment ion in the Targeted Top-Down workflow have been introduced. These metrics aim to enhance the confidence of fragment ion assignments while also helping remove poorly fitting matches.
New Reporting Format
We are seeking user feedback on the new reporting format. We have put together example templates and PDF exports, but would love to hear what you all need.
Publication Corner!
Check out the latest application notes and publications using ProSight Native:
Fast and Accurate Charge State Deconvolution of Protein Mass Spectra
In this publication, we highlight the strengths of kDecon and benchmarks it against other software. kDecon is an advanced iterative algorithm designed to deliver exceptional mass accuracy and unrivaled sensitivity for low-abundance proteoforms in complex spectra during deconvolution. In benchmarking studies, kDecon outperformed existing solutions with up to 7× fewer false positives and at least 20× faster processing, all while maintaining best-in-class precision. These capabilities make kDecon a powerful engine for routine, high-throughput intact mass profiling and deeper proteome coverage.
