Recently, the library-free approach has become one of the methods of choice for the proteomic analysis of DIA data. It simplifies the workflow allowing users to skip a DDA acquisition for the generation of a library. However, the various library-free workflows available in the field are significantly more computationally expensive.

Presenter: Lukas Reiter
Date: November 7

The poster discusses how plasma samples were measured using Biognosys’ TrueDiscovery workflow. Due to the particular protein abundance distribution in human plasma substantial improvements in proteome depth could be achieved allowing to profile more than 4000 proteins using a single shot mass spectrometry workflow.

Trapped ion mobility spectrometry (TIMS) extends conventional LC-MS/MS proteomic workflows with an additional ion mobility dimension. Next to the benefits of signal separation, the implementation of TIMS in Bruker timsTOF instruments has demonstrated that collisional cross section (CCS) values of peptides are highly reproducible and can be used as orthogonal coordinates to retention time and ion m/z values for targeted data extraction in data-independent acquisition (DIA) workflows, or as additional metric for rescoring in spectrum-centric database searches.

Neural networks have been extensively used in the proteomics field and their role on improving identifications is rapidly becoming more relevant. DeepiRT is a neural network designed to predict Indexed Retention Time (iRT) (Escher, 2012) for a given precursor based on its modified sequence.

Presenter: An-phi Nguyen

Date: Tuesday, Sep 19, 2023, 11:45 AM – 1:00 PM
Session: PP01

Poster WP 014 presented at ASMS 2022

Presenter: Dariush Mollet
Session: Artificial Intelligence in MS Instrumentation and Applications
Date: Wednesday, June 8

This poster delves into the ULTRA-DEEP EXPLORATION OF HUMAN TISSUE PROTEOMES, where 20025 protein groups were identified across all 22 tissue samples (19 healthy and 3 cancer). The poster concludes that the qualitative human tissue digital proteome serves as a rich resource that can be mined for various applications such as basal protein expression, different proteoforms, PTMs etc.

Presenter: Damiano Robbiani

Date: Thursday, June 8
Topic area: Data-Independent Acquisition II

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