BSI, dedicated to proteomics and biopharmaceuticals, provides world-leading mass spectrometry data analysis software powered by machine learning and advanced algorithms to accelerate biological research and drug discovery.
We are honoured to be invited to host the PEAKS Training Workshop on October 10–11, delivering in-depth, cutting-edge training to take you into the world of Deep Proteomics! We welcome your participation!
Register here: http://aohupo2025.com/register (be sure to select PEAKS Online Training during registration)
Course Highlights
- AI + Proteomics
- Deep proteome sequencing with DIA
- Dark Immunopeptidome
- Automation to enable high-throughput
Introduction
For the 2025 CNHUPO/AOHUPO Joint Conference in Guangzhou, the PEAKS two-day workshop will revolve around the theme Navigating the Protein Universe: Toward New Biology and Precision Medicine, exploring the dark proteome and peptidome in depth.
Over the past few years, large-scale proteomics efforts have allowed us to begin to understand phenotype at a protein level. In contrast to about 20,000 protein-coding genes in the human genome, there are over 100,000 different proteins and, as a result of alternative splicing, hundreds of thousands of protein isoforms (variants) in the human body. Proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins. It comes the revolution in high-throughput proteomics with artificial intelligence (AI) models.
In PEAKS Online training workshop, we are going to introduce AI models for high-throughput proteomics with deep coverage at proteoform level, by integrate alternative MS approaches with complementary database search and de novo sequencing data analysis. This training is highly suitable for both newcomers who have just entered the AI-empowered proteomics field and experienced researchers engaged in proteomics studies of large cohort samples.
| Day 1 | Day 2 | |
|---|---|---|
| 9:00 | Deep Learning-Based de novo Sequencing and Database Search for In-Depth and High-Throughput Proteomics | TMT and SILAC Data Analysis |
| 9:45 | Confident PTM and Sequence Variants Profiling | PEAKS GlycanFinder Walkthrough - Glycan Profiling with Structural Resolution |
| 10:30 | Coffee Break | Coffee Break |
| 11:00 | Multi-Omics Enabled Immunopeptidome with Higher Accuracy and Sensitivity | Hands-on |
| 11:45 | Streamlined Proteomics Workflow with DIA | Peptide de novo Sequencing |
| 12:30 | Lunch | Lunch |
| 13:30 | Uncover Dark Peptidome/Proteome from DIA Data with PEAKS | Deep Proteoform Profiling with Intact, Top-Down and Bottom-Up |
| 14:15 | Cloud-Based Scalable Data Analysis of Large Cohort Proteomics | Protein de novo Sequencing |
| 15:00 | Hands-on | Hands-on |
Highlights of the training course:
- Uncover dark peptidome/proteome from DIA data by a novel AI model to identify peptide sequence variants and novel peptides directly from complex DIA spectra while rigorously controlling the false discovery rate.
- Learn the automation of data analysis of large-scale cohort project to obtain in-depth proteomics and proteogenomics insights for throughput of discovery and targeted mass-spectrometry-based technologies
- Demo how to integrate intact protein analysis, Top-Down and Bottom-Up approaches, to enable comprehensive proteoform characterisation, including alternative splicing, modifications, and variants.
Deep Learning-Based de novo Sequencing and Database Search for In-Depth and High-Throughput Proteomics
Integrating database search and de novo sequencing and combining multiple enzyme digests facilitated deeper proteome coverage up to a million unique peptides from 15,000 protein groups, with a median sequence coverage of approximately 80%.
Confident PTM and Sequence Variants Profiling
Leveraging AI-powered scoring models, PEAKS achieves ultra-high confidence in identifying post-translational modifications (PTMs) and sequence variants, addressing the common issue of sensitivity and accuracy in low-abundance modification or variant detection.
Multi-Omics Enabled Immunopeptidome with Higher Accuracy and Sensitivity
Integrating LC-MS/MS data with next-generation sequencing (NGS) results, PEAKS enables comprehensive immunopeptidome profiling—overcoming the limitation of single-technology approaches and ensuring accurate identification of MHC-bound peptides for cancer immunotherapy research.
Stream-lined Proteomics Workflow with DIA
Spectral library search and library-free search are the two major approaches for DIA data analysis. Enhanced by de novo sequencing, PEAKS DIA data analysis provides you deep coverage.
Uncover Dark Peptidome/Proteome from DIA Data with PEAKS
In addition to library search and direct database search, we present a novel computational method to identify peptide sequence variants and novel peptides directly and solely from complex DIA spectra while rigorously controlling the false discovery rate.
Deep Proteoform Profiling with Intact, Top-Down and Bottom-Up
By integrating intact protein analysis, Top-Down (TD), and Bottom-Up (BU) approaches, PEAKS enables comprehensive proteoform characterisation (including isoforms, PTM combinations)—a breakthrough for understanding proteome complexity that single-method tools cannot achieve.
PEAKS GlycanFinder Walkthrough - Glycan Profiling with Structural Resolution
Unlike generic tools that only detect glycan presence, GlycanFinder provides structural-level resolution of glycans (e.g., linkage, branching), solving the key challenge of characterising complex glycan structures in glycoproteomics research.
Cloud-Based Scalable Data Analysis of Large Cohort Proteomics
PEAKS Online enables the automation of large-scale cohort project with in-depth proteomics and proteogenomics analyses and throughput of discovery and targeted mass-spectrometry-based technologies.
Additionally, Q&A sessions will be held after each presentation to address participants’ specific challenges. Whether you are new to proteomics data analysis or seeking to refine your expertise, this immersive workshop will equip you with practical tools to optimise MS workflows—leveraging PEAKS unique strengths in database-independent analysis, multi-technology integration, and high-confidence detection of complex proteomic features.
Want to know more? Request more details We’ll be happy to answer any of your inquiries today.