ASMS 2024 & User Meeting (June 2–6, 2024)

At Bioinformatics Solutions Inc. (BSI) it is our mission to advance discovery proteomics and glycoproteomics with deep learning enabled software solutions and world leading mass spectrometry services. At this year’s ASMS, we are excited to share our latest versions of PEAKS Studio and PEAKS Online and showcase the expansion of our lab services with new options like, DeepImmu Immunopeptidomics Discovery Service and PEAKS AB Polyclonal Antibody Sequence Service. Schedule a meeting with a member of the PEAKS Team at or join us at booth #302.

PEAKS Users’ Meeting

When: Sunday, June 2, 12:00 pm – 4:30 pm PDT
Where: Sheraton Park Hotel at the Anaheim Resort, 1855 S Harbor Blvd, Anaheim, CA 92802, United States

BSI has the privilege to welcome Andy Qi Ph.D. (NIH) Darshit Shah MSc. (Regeneron Pharmaceuticals, Inc.), Richard Kay Ph.D. (University of Cambridge), and John Muchena Ph.D. (Abbott Laboratories) to learn how they harness PEAKS in their labs. During the Users’ Meeting, the PEAKS team will also be presenting the latest features developed in PEAKS 12 and the newest options offered in our Service Lab. Following the presentations, PEAKS will be hosting its Mix and Mingle on the patio. Food and drinks included!

PEAKS on the Exhibit Floor

Visit booth #302
June 2: 7:45 pm – 9:00 pm
June 3–5: 9:00 am – 5:00 pm
June 6: 9:00 am – 2:30 pm
Anaheim Convention Center, 800 W Katella Ave, Anaheim, CA 92802, United States

Software Highlights

At this year’s ASMS, users will see how we have furthered the deep learning revolution in PEAKS Studio and PEAKS Online. In PEAKS 12, we have integrated AI to advance peptide de novo sequencing, PEAKS DIA Workflow, PEAKS DB, and DeepNovo Peptidome for immunopeptidomics.

  • In this new version of PEAKS users will experience the most accurate and fastest peptide de novo sequencing available in any PEAKS product. PEAKS has been known as the gold standard for automated peptide de novo sequencing for many years but with the new GPU-enabled  “DeepNovo”, de novo sequencing in PEAKS is the best it has ever been.
  • Deep learning has been integrated into our DIA workflow for spectral library search, database search, and de novo sequencing. In this version, users can expect PEAKS DIA workflow to be faster, increased sensitivity and accuracy, and better support for short gradients.
  • DeepNovo Peptidome supports both DDA and DIA data analysis and is a specialised workflow for immunopeptidomics. In this version, we have integrated the latest DeepNovo to improve the speed and provide the complete peptide identity, including peptides with a variety of modifications, sequence variants, and novel peptide.
  • PEAKS provides a unique de novo-assisted database search called PEAKS DB to improve both sensitivity and accuracy. The users have the option to include the deep learning boost for MS2 rescoring and improving the number of identifications by ~10%.

Service Highlights

This year we moved to a new facility and have released two new services in our lab called DeepImmu Immunpeptidomics Discovery Service and PEAKS AB Polyclonal Antibody Sequencing. Both solutions require a strong de novo sequencing solution to accurately obtain the amino acid sequence directly from LC-MS/MS data, and as the developers of PEAKS de novo sequencing, we harness our bioinformatics, mass spec and AI expertise to offer these services professionally to researchers around the world.

DeepImmu Immunpeptidomics Discovery Service

For our Immunopeptidomics service we perform cell lysis, tissue and plasma sample processing, MHC peptide purification, LC-MS/MS, peptide identification, sequence motif generation, and binding affinity and immunogenicity prediction. This service also includes quality control tests to ensure accurate results. Our advanced software algorithms and PEAKS DeepNovo Peptidome workflow provides accurate, sensitive, and reproducible results for immunopeptide identification and quantification.

PEAKS AB Polyclonal Antibody Sequencing

In our lab, we have developed a complete workflow that integrates multi-dimensional LC with intact, top-down, and bottom-up data to accurately de novo sequence antibody mixtures. Our complete platform harnesses deep learning technology and innovative software algorithms, called PolySeq.AI, to handle the complexity in top-down proteomics data, while combining intact and bottom-up data into the final sequencing results. This complete solution for sequencing antibody mixtures will be offered under PEAKS AB Polyclonal Antibody Sequencing Service by BSI Mass Spec Lab.

PEAKS GlycanFinder: Glycan Profiling Lab Service

Our service is catered to your glycoproteomic needs utilising our optimised protocols and advanced PEAKS® GlycanFinder software. Our workflows accommodate various sample types ranging from gel pieces to purified proteins to cell lysate. We offer a service tailored to the analysis of purified proteins that consists of N- and O-linked glycopeptide mapping that can additionally be supported with intact mass glycoform data. Additionally, we perform optimised glycan enrichment procedures for enhancing glycoproteomic analysis of complex samples and cell lysates.

Conference Posters

TP 566 An AI-driven, proteogenomics-based and complete workflow for novel neoantigen discovery
Authors: Qing Zhang [1], Kyle Hoffman [1], Sahar Rabinoviz [1], Peng Chao [2], Haibo Bian [1], Wenting Li [1], Lei Xin [1], Baozhen Shan [1]
[1] Bioinformatics Solutions Inc., Waterloo, ON
[2] Baizhen Biotechnology (Shanghai) Co., Ltd., Shanghai 201112, China

ThP 058 A Bayesian model for estimating the posterior error probability and the false discovery rate of de novo peptide sequencing
Authors: Hieu Tran [1], Rui Qiao [1], Lei Xin [1], Baozhen Shan [1]
[1] Bioinformatics Solutions Inc., Waterloo, ON

WP 047 Revolutionizing Proteomics: Ultra-Fast, High-Accuracy Peptide Sequencing with Enhanced GraphNovo Algorithm
Authors: Zeping Mao [1], Lei Xin[1], Shengying Pan [1], Baozhen Shan [1]
[1] Bioinformatics Solutions Inc., Waterloo, ON

WP 704 Combining Top-Down and Bottom-Up Mass Spectrometry Paves the Way for High Throughput Polyclonal Antibody Sequencing
Authors: Lei Xin [1], Peng Chao [2], Jun Ma [2], Shuyang Zhang [1], Zihao Wang [1], Wenting Li [1], Kyle Hoffman [1], Ailee Aihemaiti [1], Baozhen Shan [1]
[1] Bioinformatics Solutions Inc., Waterloo, ON
[2] Baizhen Biotechnology (Shanghai) Co., Ltd., Shanghai 201112, China

MP 451 Confident identification of proteome-wide low-level mutations using PEAKS 11.5
Authors: Kyle Hoffman [1], Julie Genereaux [2], Lei Xin [1], Zia Rahman [1], Christopher J Brandl [2], Patrick O’Donoghue [2], Baozhen Shan [1]
[1] Bioinformatics Solutions Inc., Waterloo, ON
[2] Western University, London, ON

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