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Human Proteome Organization
World Congress (HUPO)
September 17 – 21, 2023 | Busan, South Korea 

At this year's HUPO World Congress, MSAID will showcase major feature updates to CHIMERYS, the intelligent search algorithm for proteomics. Don't miss the new capabilities!


We are excited to announce that MSAID will be showcasing its latest software developments at the upcoming Human Proteome Organization World Congress (HUPO) in Busan, South Korea in September.



  • PP05.24: Analyzing data-independent acquisition (DIA) data one experimental spectrum at a time

    Date and Time: Sep 20, 2023 | 11:45 AM - 1:00 PM
    Session: Poster Viewing with Coffee Break Wednesday
    DIA spectra are inherently chimeric as they contain fragment ions from multiple peptide precursors, some of which will be shared. Peptide-centric approaches typically remove these shared fragment ions based on correlations with precursor ions over retention time. We have previously developed a technique to deconvolute chimeric DDA spectra that does not rely on such correlations and can distribute shared fragment ion intensities between precursors instead of discarding them. We demonstrate that this approach extends to any chimeric MS2 spectrum, enabling the consistent analysis of DDA and DIA data.

  • PP05.138: Digging deeper into phosphoproteomes through AI-driven deconvolution of chimeric spectra

    Date and Time: Sep 20, 2023 | 11:45 AM - 1:00 PM
    Session: Poster Viewing with Coffee Break Wednesday
    The analysis of phosphopeptides requires accurate identification and correct localization of the post-translational modification within the peptide. Here, we extend the capabilities of our deep-learning framework to accurately predict physicochemical properties of phosphorylated peptides and demonstrate the usefulness of these predictions in our search algorithm enabling the analysis of such analytes.

  • PP05.34: Fully automated and spectrum-centric processing of parallel reaction monitoring (PRM) data

    Date and Time: Sep 20, 2023 | 11:45 AM - 1:00 PM
    Session: Poster Viewing with Coffee Break Wednesday
    Targeted mass spectrometry assays are vital for the sensitive quantification of low-abundant peptides and biomarkers. Parallel reaction monitoring (PRM) is a targeted technique where full fragmentation spectra from predefined isolation windows are monitored over retention time. Identification is typically performed by correlating data with a spectral library, and quantification uses area under the curve from extracted ion chromatograms (XICs) of chosen fragment ions, requiring expert knowledge and frequent manual refinement. Here, we present an automated algorithm for PRM data analysis, abstracting manual fine-tuning in the development or execution of targeted assays.

  • PP01.125: CHIMERYS server: deploying the power of the cloud in your basement 

    Date and Time: Sep 18, 2023 | 11:45 AM - 1:00 PM
    Session: Poster Viewing with Coffee Break Monday
    CHIMERYS is a cloud-based search engine on Amazon Web Services (AWS) with a client interface for Proteome Discoverer software (PD). While AWS offers scalability and accessibility, transferring large data or user preference for in-house data storage may limit cloud service practicality. To address this, we adapted CHIMERYS as an on-premises solution for single servers and HPC environments, combining the best of both worlds. 


Find more information about our participation in conferences and events.



US HUPO 2024
Bridging ‘Omics To Function

March 9 – 13, 2024
Portland, OR, USA


Conference of the German Society for Mass Spectrometry (DGMS)

March 10 – 13, 2024
Freising, Germany


EuBIC European Bioinformatics Community For Mass Spectrometry

January 15 – 19, 2023
Winterberg, Germany