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ProteomicsEvaluation of the Effect of Trypsin Digestion Buffers on Artificial Deamidation
This work comprehensively compared 50 mM of ammonium acetate (pH 6), Tris-HCl (pH 8), ABC and TEAB as in-solution trypsin digestion buffers. Both iTRAQ quantification and label-free results indicate that ammonium acetate (pH 6) is more suitable than other buffers for studying endogenous deamidation ...
ORGANISM(S): Rattus norvegicus (Rat) 
2022-02-28 | PXD001650 | Pride
Rat Kidney Artificial deamidation 
ProteomicsRevisiting the effect of trypsin digestion buffers on artificial deamidation
Deamidation of asparagine and glutamine residues occurs spontaneously, accelerated by adjacent amino acid residues and influenced by pH, temperature, and incubation time. Standard proteolytic digestion induces significant deamidation, which is especially problematic in bottom-up proteomic studies. T...
ORGANISM(S): Mus musculus (Mouse) 
2025-03-11 | PXD054603 | Pride
De-glycopeptides Chemical deamidation De-glycoproteomics 
ProteomicsRapid High-Throughput Antibody Analysis Using Microwave-Assisted Digestion
Monoclonal antibodies (mAbs) are a major class of biotherapeutic proteins that have been extensively developed over the past decade, resulting in improved standards of care for multiple diseases. Regulatory agencies recommend a Quality by Design (QbD) approach for manufacturing therapeutic proteins,...
ORGANISM(S): Homo sapiens (Human) 
2026-01-26 | PXD067893 | Pride
Data independent acquisition Post translational modifications Antibodies Data dependent acquisition Microwave-assisted digestion 
ProteomicsStudy Samples Dendritic Cell MHC II presentation by LC-MSMS
MAPPs data was used to construct an artificial neural network (ANN) model for MHC class II antigen presentation. Using Infliximab and Rituximab, the model demonstrated an unprecedented performance for predicting MAPPs and CD4 T cell epitopes, complementing results from MAPPs assays and outperforming...
ORGANISM(S): Homo sapiens (Human) 
2020-06-24 | PXD018303 | Pride
Lc-msms Mhc-associated peptide proteomics (mapps) Mhc ii presentation Dendritic cells 
ProteomicsArtificial Intelligence in proteomic profiling of Cerebrospinal fluid from extraventricular drainage in child Medulloblastoma
Medulloblastoma (MB) is the most common pediatric malignant central nervous system tumor. Overall survival in MB depends on treatment tuning. There is the need for biomarkers of residual disease, and recurrence. We analysed the proteome of waste cerebrospinal fluid (CSF) from extraventricular draina...
ORGANISM(S): Homo sapiens (Human) 
2022-10-14 | PXD035292 | Pride
Cerebrospinal fluid Central nervous system Mass spectrometry Proteomics Medulloblastoma 
ProteomicsSupporting information for tryptic EPO glycopeptide LC-MS analysis via cysteine aminoethylation
Supplementary information for a technical note describing the application of cysteine aminoethylation for the site-specific glycosylation analysis of recombinant human EPO using trypsin as sole protease.
ORGANISM(S): Cho Cells 
2020-04-21 | MSV000085318 | MassIVE
UnknownSpecific Post-Translational Modifications of VDAC3 in ALS-SOD1 Model Cells Identified by High-Resolution Mass Spectrometry.
Not available
S-EPMC9784795 | biostudies-literature
UnknownCombining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins.
Not available
S-EPMC10965067 | biostudies-literature
ProteomicsA Genetically Programmed Electronic Marine Biofilm
Dataset accompanying the publication "A Genetically Programmed Electronic Marine Biofilm" by Bird et al. submitted for review to ACS Synthetic Biology. These data represent proteome profiles of multiple strains of Marinobacter atlanticus CP1 which are featured in the manuscript's Supporting Informa...
ORGANISM(S): Marinobacter Sp. Cp1 (ncbitaxon:1671721) Marinobacter Atlanticus Cp1 
2022-07-28 | MSV000090010 | MassIVE
UnknownDevelopment of an LC-MS/MS peptide mapping protocol for the NISTmAb.
Not available
S-EPMC5830484 | biostudies-literature
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