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ProteomicsMonitoring mAb proteoforms in mouse plasma using an automated immunocapture combined with top-down and middle-down mass spectrometry
We propose here a workflow based on an automated immunocapture followed by top-down and middle-down LC-MS/MS approaches to characterize mAb proteoforms spiked in mouse plasma. We demonstrate the applicability of our workflow on a large concentration range using pembrolizumab as a model. We also comp...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2024-08-27 | PXD040896 | Pride
Immunocapture Monoclonal antibody Proteoforms Middle-down mass spectrometry Top-down mass spectrometry 
ProteomicsEnhance proteoform sequence coverage by using top-down proteomics and middle-proteomics
Using in-source fragmention in top-down proteomics experiments and limited digestion time for middle-down experiments to enhance the sequence coverage.
ORGANISM(S): Bos taurus (Bovine) Equus caballus (Horse) 
2026-02-17 | PXD068831 | Pride
Lc-ms Mdp Tdp 
ProteomicsDynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics
We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval s...
ORGANISM(S): Caenorhabditis elegans 
2015-11-02 | PXD002525 | Pride
C. elegans Lifecycle Post-translational modifications Histones Middle-down proteomics 
ProteomicsMiddle-down MS analysis of intact and clipped histone H3 proteoforms
There is growing evidence that proteolytic cleavage of histone N-terminal tails, known as histone clipping, influences nucleosome dynamics and functional properties. Using middle-down MS analysis we characterized intact and proteolytically processed histone H3 proteoforms isolated from human hepatoc...
ORGANISM(S): Homo sapiens (Human) 
2022-03-14 | PXD002535 | Pride
Liver Hepg2/c3a Middle-down ms Histone post-translational modifications 
ProteomicsTowards an optimized workflow for middle-down proteomics
Detailed description of an optimally tuned workflow for high throughput middle-down proteomics with the currently available state-of-the-art instrumentation. In this work we describe and critically evaluate the limits of an optimized workflow for the detection of middle-range peptides. First, the wo...
ORGANISM(S): Homo sapiens (Human) 
2017-03-16 | PXD004910 | Pride
Human Middle-down proteomics Orbitrap fusion 
ProteomicsA multi-parameter optimization in middle-down analysis of monoclonal antibodies by LC-MS/MS
In antibody-based drug research, regulatory agencies request a complete characterization of antibody proteoforms covering both the amino acid sequence and all post-translational modifications. The usual mass spectrometry-based approach to achieve this goal is bottom-up proteomics, which relies on th...
ORGANISM(S): Homo sapiens (Human) 
2023-03-15 | PXD038619 | Pride
Orbitrap ms Middle-down proteomics Monoclonal antibody Intact proteins Lc-ms/ms 
ProteomicsGeLC-FAIMS-MS Workflow for In-Depth Middle-Down Proteomics
Middle-down proteomics is an analytical approach whereby protein samples are digested with proteases such as Glu-C to generate large peptides (>3 kDa) that are then analyzed by mass spectrometry. This method is useful for characterizing high-molecular-weight proteins that are difficult to detect by ...
ORGANISM(S): Homo sapiens (Human) 
2024-11-20 | PXD041358 | Pride
Glu-c digestion Proteoform Middle-down proteomics Lc-faims orbitrap mass spectrometry Peppi-ms Anexsp 
ProteomicsMulti-level – Intact, Subunits, and Peptides – Characterization of Antibody-Based Therapeutics by a Single-Column LC-MS setup
A comprehensive characterization of biotherapeutics, mandated by regulatory authorities, require analyses of a protein drug at multiple structure levels. Such multi-level characterization can be performed by mass spectrometry (MS), with established conventional MS-based assays of product quality att...
ORGANISM(S): Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus) 
2025-02-26 | PXD054948 | Pride
Subunits Intact Lc-ms Ead C4-column Peptides 
ProteomicsQuantitative middle-down MS analysis of histone H3 proteoforms throughout lifespan in mice
Replication-independent deposition of histone variant H3.3 into chromatin is essential for many biological processes, including development, oogenesis and nuclear reprogramming. Unlike replication-dependent H3.1/2 isoforms, H3.3 is expressed throughout the cell cycle and becomes enriched in postmito...
ORGANISM(S): Mus musculus (Mouse) 
2017-07-28 | PXD005300 | Pride
Histone modification landscape C57bl/6 mice H3 variants Middle-down ms 
ProteomicsFluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics
Cellular reprogramming remodels the gene expression program by re-setting the epigenome of somatic cells into an embryonic-like state. Post-translational modifications of histones play an important role in this process. We previously used ChIP-seq to profile the distribution of specific histone H3 m...
ORGANISM(S): Mus musculus (Mouse) 
2015-08-17 | PXD002062 | Pride
Proteomics Middle-down Histone h4 Cellular reprogramming Post translational modifications 
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