BSI is heading to the CASSS Mass Spec 2026 conference this week!

Date: Sept 16^th-18^th
Venue: Hilton Washington DC/Rockville Hotel, Rockville, Maryland
Booth No: 13

Stop by 𝗕𝗼𝗼𝘁𝗵 𝟭𝟯 to connect with the BSI team and learn about the latest advances in our 𝗣𝗘𝗔𝗞𝗦 platform, as well as our brand-new 𝗟𝗮𝗯 𝗦𝗲𝗿𝘃𝗶𝗰𝗲𝘀 tackling multispecific antibody characterization and more!

Don't miss our poster: "𝗘𝘃𝗮𝗹𝘂𝗮𝘁𝗶𝗻𝗴 𝗖𝗿𝗶𝘁𝗶𝗰𝗮𝗹 𝗤𝘂𝗮𝗹𝗶𝘁𝘆 𝗔𝘁𝘁𝗿𝗶𝗯𝘂𝘁𝗲𝘀 𝗼𝗳 𝗠𝘂𝗹𝘁𝗶𝘀𝗽𝗲𝗰𝗶𝗳𝗶𝗰 𝗔𝗻𝘁𝗶𝗯𝗼𝗱𝗶𝗲𝘀 𝗯𝘆 𝗠𝘂𝗹𝘁𝗶-𝗟𝗲𝘃𝗲𝗹 𝗠𝗮𝘀𝘀 𝗦𝗽𝗲𝗰𝘁𝗿𝗼𝗺𝗲𝘁𝗿𝘆", showcasing how our integrated MS-based approach tackles correct pairing, PTM/glycan analysis, sequence validation, and more.

𝗧𝗶𝘁𝗹𝗲: Evaluating Critical Quality Attributes of Multispecific Antibodies by Multi-Level Mass Spectrometry
𝗦𝗲𝘀𝘀𝗶𝗼𝗻𝘀: Wed, Sept 16: 9:45 AM – 10:45 AM; Thurs, Sept 17: 9:45 AM – 10:15 AM
𝗣𝗼𝘀𝘁𝗲𝗿 𝗻𝗼: 115

Come say hi, we would love to learn more about your research and see if our PEAKS software or lab services could be good fit!
See you in Rockville, Maryland!

Learn more and register here: https://www.casss.org/mass-spectrometry

A recent paper in Nature, from the Church Lab at Harvard Medical School & the Wyss Institute introduces AGENTEX (automated genetic tRNA expansion), a robotic, multiplexed tool for building and testing new genetic codes in cell-free translation systems.

Radford et al. revisited a long-standing assumption that the tRNA 3′ CCA end, where amino acids attach and tRNAs dock into the ribosome, must be intact for aminoacylation. Using a new sequencing method they developed, tSCAN, the team varied the tRNA 3′ end across the entire E. coli tRNA set and found that most non-CCA tRNAs ("otRNAs") were still efficiently charged by natural synthetases, far more tolerant to mutation than previously believed.

Building on this, the authors engineered ribosomes (G2251C/G2553C, "CGA ribosomes") that specifically accommodate otRNAs while ignoring native tRNAs. Pairing otRNA pools with these orthogonal ribosomes gave rise to AGENTEX, run end-to-end on an automated OT-2 robotic platform. Using it, the team compressed the 64-codon code down to as few as 21–22 codons, incorporated a non-standard amino acid via amber suppression, and showed the compressed and standard genetic codes could run in parallel, without "crosstalk". Confirming this "zero crosstalk" required proteomics sensitive enough to catch rare mistranslation events. The team relied on PEAKS Studio 13 to search high-sensitivity LC-MS/MS data against custom libraries covering every possible amino acid substitution their engineered codes could introduce, showing that the ribosome, not the synthetase, is the real gatekeeper of genetic code fidelity.

Congratulations to the Church Lab on this remarkable accomplishment! This breakthrough technology overturns decades of understanding of how transfer RNAs (tRNAs) help turn the genetic code into proteins and takes a leap forward by making 34 codons customizable, allowing researchers to make proteins with up to 34 different amino acids much faster and safer.

BSI is delighted to witness the application of PEAKS software in this pioneering research within synthetic biology! We sincerely appreciate our ongoing collaboration with Dr. Bogdan Budnik and look forward to future advancements.

Read the full article here: Radford, F., Sapers, N., Burgess, H. M., Ort, L., Budnik, B., & Church, G. M. (2026) Automated prototyping of genetic codes. Nature. https://doi.org/10.1038/s41586-026-10949-y

Date: August 23^th–25^th, 2026
Venue: Centre des Congrès de Lyon, France
Booth No: 48

We're excited to announce that BSI will be at the International Mass Spectrometry Conference (IMSC) 2026 in beautiful Lyon, France! Come find us at Booth 48!

This year, we're showcasing exciting new improvements to our platforms, designed to help you work smarter, faster, and with even greater precision. Our team will be on hand throughout the event to walk you through what's new, answer your questions, and talk about how these updates can support your research and workflows.

Whether you're a longtime partner or just discovering BSI, we'd love to connect. Stop by to see the latest in PEAKS firsthand and chat with our team!

We can't wait to see you in Lyon!

Learn more and register here.

PEAKS^® Online 13.5 introduces redesigned DDA and DIA workflows for streamlined and user-friendly experience with enhanced algorithms. With a fresh UI, increased data and system stability, and simplified parameter selection users can take their analyses to new heights! CFR compliance readiness ensures data integrity, security, and audit preparation in any clinical or industrial setting!

Exclusive to PEAKS Online 13.5 are the Automated Large-Cohort and Real-time Quality Control workflows, providing a comprehensive interface for automated instrument-to-software data processing and real-time quality assessment.

Automated Large-Cohort Analyses

PEAKS Online 13.5 delivers an automated, real-time proteomics data analysis pipeline with instrument monitoring, streamlined data processing, and an accumulative results overview to accelerate QC and exploration of large-cohort datasets.

Real-time Quality Control

Exclusive to PEAKS Online, this pioneering workflow incorporates Instrument Daemon functionality for automated screening of QC samples. The streamlined workflow enables immediate assessments of technical variation throughout acquisition, and users are notified immediately if QC attributes fail to meet the defined standards.

Open PTM Search

PEAKS' Open PTM Search algorithm delivers an efficient, sensitive, and unbiased solution for characterising unknown PTMs, supporting a wide range of experimental setups, including various digestion modes and isotopic labelling.

Ready to see what’s possible with Online 13.5?
Check out the full list of features and enhancements on our launch page.

Discover faster insights, deeper results, and more flexibility than ever before.

The PEAKS Team
Bioinformatics Solutions Inc.

Date: June 23^th–25^th, 2026
Venue: Westin San Diego Bayview, San Diego, CA, USA
Booth No: 6

We are headed back to sunny San Diego, to attend the 8th Annual T-Cell Engager Therapeutics Summit—and we're coming with a lot to share!

Join us at Booth 6 as we showcase the latest advancements in our PEAKS software platforms, available for various proteomics workflows. Hear from our experienced team members about how our advanced lab solutions are providing deeper insight to researchers. Don't miss our poster presentation as our talented Applications Manager, Kyle Hoffman, will also be talking about our new developments to our lab services methodologies.

Whether you're deep into bispecific development or just curious about what's new in proteomics, we'd love to connect and talk science!

Learn more and register here.

Smarter Workflows, Deeper Discovery.

We are proud to introduce PEAKS GlycanFinder 3.5, the latest evolution of our glycoproteomics and glycomics software platform. This release brings powerful new features and workflow improvements to take your research to the next level.

Glycan de novo-assisted Database search

PEAKS GlycanFinder exclusive glycan de novo sequencing-assisted database search workflow integrates glycan de novo and glycopeptide database search, delivering superior sensitivity of glycopeptide identifications while allowing for the discovery of hidden glycopeptides. Evaluating each MS2 spectrum with two independent approaches results in enhanced confidence and increased glycoproteome depth. Both composition and structure based resolution is available.

Glycan de novo

Novel Glycan de novo workflow allows for glycopeptide deciphering and the analysis of both unknown proteins & unknown glycans. It takes advantage of both peptide backbone and glycan sequencing, allowing users to analyse unknown proteins and glycans. Here an example is shown of a novel glycan identified by our glycan de novo function, which was absent from the database.

Glycosylated Peptidome

A specialised and unique workflow for the discovery and characterisation of completely novel glycan profiles for HLA peptides, without any need for a glycan database. For example, PEAKS GlycanFinder was to able to discover an N- glycosylated peptide as a putative biomarker for drug responses (Phenomics. 1(6):269-284. (2021)).

InChorus—Cross Engine Consensus Results

Our improved InChorus feature combines results from multiple glycan search engines, highlighting both consensus and unique glycopeptide findings. This tool extracts glycoPSMs from external search engine result outputs, visualises spectrum level overlaps for each PSM, and provides a Consensus score - metric that evaluates the consistency and confidence of G-spectral matches across multiple search engines.

Ready to see what’s possible with PEAKS GlycanFinder 3.5?
Check out the full list of features and enhancements on our launch page.

Discover faster insights, deeper results, and more flexibility than ever before.

The PEAKS Team
Bioinformatics Solutions Inc.

PEAKS Studio 13.5 introduces exciting new features across Discovery and Targeted workflows! Open PTM in DDA workflows enables unknown PTM characterisation. Additionally, Multi-round Search in DDA Proteome provides access to comprehensive multi-species analysis. With improved DIA performance and deeper discovery with PTM profiling without the need for a spectral library, PEAKS Studio provides users with the unprecedented depth required for next-level proteomics research.

Check out all the new features below!

Greater Depth with Open PTM in DDA Workflows

PEAKS' novel Open PTM Search algorithm delivers an efficient, sensitive, and versatile solution for characterising unknown PTMs, providing an unbiased PTM profile. Here, our algorithm performs a wide precursor mass tolerance on unmatched high-quality spectra.

Unlock the Dark Proteome with DIA PTM

Push beyond traditional spectral library and database searches into the dark proteome, uncovering deep insights into PTM profiles and novel peptides directly from DIA data without the use of a spectral library. By leveraging our de novo-assisted sequencing logic, unbiased identification of unlimited PTMs is now possible in our DIA workflow.

Search Multi-Species with Multi-Round Search

An additional database search option for DDA Proteome re-analyses unassigned spectra with good de novo tags, uncovering additional peptide identifications beyond the initial database search.

Improved DIA Performance

Our enhanced DIA will accelerate your discovery, ensuring accurate and comprehensive results to provide complex biological insight. Improved performance with high reproducibility quantifying protein groups with CV <10%.

Additional Features

Ready to see what’s possible with PEAKS Studio 13.5?
Check out the full list of features and enhancements on our launch page.

Discover faster insights, deeper results, and more flexibility than ever before.

The PEAKS Team
Bioinformatics Solutions Inc.

ProteoformX 1.5.1 is Here!

We are excited to announce new updates to ProteoformX, introducing powerful new features across Intact, Top-down, and Bottom-up analyses. Customisable workflows across each module to fit your unique research needs. CFR compliance readiness ensures data integrity, security, and audit preparation in any clinical or biopharmaceutical setting.

With fully integrated analytical workflows spanning the breadth of proteoform-level characterisation, from cutting-edge proteomics research to biopharmaceutical analysis, ProteoformX continues to redefine what is possible.

Intact Mass Analysis

• Use high precision mass deconvolution of protein mixtures with detailed glycoforms and PTM annotations, reporting detectable proteoforms with corresponding mass and retention time.
• Versatile visualisation options, including Heat Map view for monitoring proteoform intensity changes. Proteoform Manager for defining proteoform details, residues, and modifications.
• NEW! Batch search and Compare Analysis functions give users a streamlined interface to evaluate and compare results for QC or discovery of modifications introduced during engineering.

• NEW! Redesigned manual annotation tool delivers a significantly expanded feature set for in-depth spectral analysis of target molecular mass, delta masses between base peaks, and modification candidates.

Top-Down Search

• Achieve a comprehensive understanding of individual proteoforms by integrating Top-down and Bottom-up data analyses to balance broad screening with precise molecular detail, enabling confident sequence validation and resolution of PTM co‑occurrence.
• NEW! View Proteoform Networks showing the relationship between different proteoforms generated by one gene, including the mass shifts for the modified proteoforms.

• NEW! Add confidence level to evaluate the confidence in proteoform identification. Bottom-up analysis complements top-down data by generating peptide-level evidence, which can provide additional sequence coverage and support PTM localization.

Peptide Mapping

• Use Bottom-up proteomics to characterise protein sequences, post-translational modifications, and sequence variants at the peptide level.
• NEW! Hierarchical peptide visualisation: Organises peptide mapping results around fully digested backbone peptides, grouping related modified and variant forms together to streamline sequence coverage assessment, modification characterization, and cross-sample quantitation.

Ready to see what’s possible with ProteoformX 1.5.1?
Check out the full list of features and enhancements on our launch page.

Discover deeper insights, versatile visualisations, and comprehensive results, with more flexibility than ever before!

The PEAKS Team
Bioinformatics Solutions Inc.

In modern proteomics, the ability to accurately decode peptides and their chemical modifications is essential—but traditional approaches are often limited to what is already known. In this paper, researchers introduce RNovA, a next-generation deep learning model that redefines how peptide sequencing can be performed.

Built on a transformer architecture, RNovA enables de novo peptide sequencing directly from mass spectrometry data, without relying on protein databases. What sets it apart is its ability to discover post-translational modifications (PTMs) in a zero-shot setting—meaning it can identify unexpected or previously unseen modifications without prior training or predefined lists.

The model combines advanced positional encoding with a sequential decision-making process, allowing it to maintain state-of-the-art accuracy while dramatically expanding discovery potential. In practical applications, RNovA successfully identified rare and biologically significant modifications, including kynurenine in clinical samples, and uncovered previously unannotated modifications in organisms lacking reference proteomes.

At BSI, we are proud of our team who collaborated on this work, contributing to an innovation that pushes the boundaries of proteomics research. By opening the door to unbiased and scalable PTM discovery, RNovA represents a major step forward in proteomics—enabling researchers to explore previously hidden layers of biological complexity and accelerate insights across disease research, microbiology, and beyond.

Mao, Z., Peng, C., Chen, Y. et al. Zero-shot de novo peptide sequencing with open posttranslational modification discovery. Nat Biotechnol (2026). doi:10.1038/s41587-026-03116-1

Abstract

De novo peptide sequencing directly infers sequences from mass spectrometry data without relying on protein databases. Although recent deep learning models can also identify posttranslational modifications (PTMs), they require labeled training data for this task. Here we introduce rotary positional embedding-enhanced de novo sequencing algorithm (RNovA), a transformer-based de novo sequencing algorithm enhanced with relative positional embeddings and a reinforcement-learning-style sequential decision framework. RNovA enables open PTM discovery in a zero-shot setting—without retraining or a predefined list of candidate residues—while maintaining state-of-the-art performance on standard benchmarks. Demonstrating this capability, we successfully identified peptides modified by kynurenine—an uncommon and biologically relevant PTM—in clinical samples from patients with RA and validated this discovery with synthetically synthesized reference peptides. Furthermore, we demonstrated open de novo PTM discovery by analyzing the bacterial strain A1232E, which lacks a reference proteome, and detected an unannotated glutamic acid modification. RNovA enables exploration of previously inaccessible regions of the proteome, including peptides with unexpected or unannotated modifications.

BSI is excited to attend ASMS 2026 in sunny San Diego, California, and we’re bringing a full line-up of opportunities to learn, connect, and explore what’s new in the PEAKS ecosystem! Throughout the conference, you’ll have the chance to hear directly from our users, meet the BSI team, and dive into the latest advancements in proteomics research and software innovation. We’re kicking things off with our User Meeting, followed by a research‑focused Breakfast Seminar—and of course, you can always find us at Booth 915 to continue the conversation.

User Meeting

Join us at our User Meeting, where our industrial and academic partners will showcase unique real‑world applications and insights from their work. The BSI team will also highlight the newest PEAKS features and developments across our software and lab services platforms.

Omni San Diego at the Ballpark, Gallery 2 & Ace Porter
Sunday, May 31^st, 12:00–4:30 p.m.

PEAKS Finder: A Software Tool for Efficient and Comprehensive Characterization of Biotherapeutics in Drug Discovery

Xianyin Lai, PhD
Senior Director, Research & Development,
Eli Lilly

Targeted immunopeptidomics without authentic synthetic peptide standards

Curt Fischer, PhD
Member of Technical Staff,
Decade Bio

Following the talks, join us for casual networking, great conversations, and a chance to meet the BSI team and PEAKS users in a more relaxed setting over light food and refreshments.

Agenda

Breakfast Seminar

Continue the conversation at our Breakfast Seminar, featuring dedicated user presentations from key researchers in discovery proteomics, glycoproteomics, and top‑down proteomics. Hear how they are leveraging PEAKS to drive cutting‑edge research and advance scientific discovery.

San Diego Convention Center, Room 2
Monday, June 1^st, 7:00–8:15 a.m.

ZT Scan DIA: a more efficient acquisition mode for high-throughput, quantitative, and PTM-resolved proteomics

Tim Heymann, PhD
Mass Spectrometry Specialist,
Max Planck Institute of Biochemistry

Advancing top-down proteomics by capillary electrophoresis-mass spectrometry and ProteoformX

Liangliang Sun, PhD
Associate Professor,
Michigan State University

Agenda

Poster Presentations

328838 - Integrating Glycan Database Search and de novo Sequencing for Unbiased Glycan Discovery
Glycoproteins I
Wednesday, June 3^rd, WP 395

327426 — Targeted immunopeptidomics without authentic synthetic peptide standards
Artificial Intelligence in MS Instrumentation and Applications I
Wednesday, June 3^rd, WP 045

327086 — A de novo sequencing approach enables tumor-wide immunopeptidomic profiling and comprehensive discovery of neoantigens from diverse origins
Informatics: Peptide ID and Quantification
Wednesday, June 3^rd, WP 452

326684 — Unleash the power of Hybrid-DIA with AI-driven software for Biomarker Discovery and Validation
Proteomics: Quantitative I 
Wednesday, June 3^rd, WP 688

329958 — Evaluating critical quality attributes of bispecific antibodies by multi-mass spectrometry
Antibodies & Antibody Drug Conjugates III
Thursday, June 4^th, ThP 045

Can't make any of our events? Come by Booth 915 to meet our team and learn more about our solutions!

We can't wait to see everyone in San Diego!