Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit

M Picciani, W Gabriel, VG Giurcoiu, O Shouman… - …, 2024 - Wiley Online Library
Abstract Machine learning (ML) and deep learning (DL) models for peptide property
prediction such as Prosit have enabled the creation of high quality in silico reference …

Real-time spectral library matching for sample multiplexed quantitative proteomics

CD McGann, WD Barshop, JD Canterbury… - Journal of Proteome …, 2023 - ACS Publications
Sample multiplexed quantitative proteomics assays have proved to be a highly versatile
means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor …

Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing

JA Paulo - Proteomics, 2022 - Wiley Online Library
Isobaric labeling has rapidly become a predominant strategy for proteome‐wide abundance
measurements. Coupled to mass spectrometry, sample multiplexing techniques using …

Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics

NB Palstrøm, AJ Campbell, CA Lindegaard… - …, 2024 - Wiley Online Library
Clinical biomarker discovery is often based on the analysis of human plasma samples.
However, the high dynamic range and complexity of plasma pose significant challenges to …

Deep Learning-Assisted Analysis of Immunopeptidomics Data

W Gabriel, M Picciani, M The, M Wilhelm - Peptidomics: Methods and …, 2024 - Springer
Liquid chromatography-coupled mass spectrometry (LC-MS/MS) is the primary method to
obtain direct evidence for the presentation of disease-or patient-specific human leukocyte …

Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes

W Gabriel, R Meelker Gonzalez, S Laposchan… - bioRxiv, 2024 - biorxiv.org
Citrullination is a critical yet understudied post-translational modification (PTM) implicated in
various biological processes. Exploring its role in health and disease requires a …