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MetabolomicsA multi-omics approach reveals functions of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees
Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved proteins that are involved in membrane trafficking. An integrated approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. The metabolomics analyses were performed in woody tissues of transgeni...
2018-01-08 | MTBLS478 | MetaboLights
ProteomicsA carrier-based quantitative proteomics method applied to biomarker discovery in pericardial fluid
Data-dependent liquid chromatography tandem mass spectrometry (LC-MS/MS) is challenged by the large concentration range of proteins in plasma and related fluids. We adapted the SCoPE method from single-cell proteomics to pericardial fluid, where a myocardial tissue carrier was used to aid protein qu...
ORGANISM(S): Homo sapiens (Human) 
2024-07-31 | PXD053450 | Pride
Carrier proteome Single-cell proteomics Biomarker discovery 
ProteomicsSingle Cell Proteomics and the Carrier Proteome Effect
Single cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method that utilizes isobaric labels to quantify multiplexed single cell proteomes. While this technique has generated great excitement, the technologies underlying SCoPE-MS - isobaric labels and mass spectrometry - comp...
ORGANISM(S): Homo sapiens (Human) 
2020-12-16 | PXD016573 | Pride
Human Lc-msms Single cell proteomics 
ProteomicsCarrier protein-enabled host cell proteome analysis (CP-HCP) with integrated isobaric tag interference filtering
We have created a CP-HCP method to characterise the carrier proteome of a host cell expression system producing recombinant protein biotherapeutic, which can be compared with the testing sample mixture containing trace amounts of host cell proteins against high-background recombinant protein and als...
ORGANISM(S): Escherichia coli 
2026-01-12 | PXD050214 | Pride
Psms Host cell proteins Ms3 Tmt Carrier proteome Multiplexed proteomics Lc-ms Co-isolation Interference Co-fragmentation Dda 
ProteomicsCarrier protein-enabled host cell proteome analysis (CP-HCP) with integrated isobaric tag interference filtering.
Here, we proposed that the use of an HCP carrier proteome could enhance the acquisition of spectra from HCPs amidst a highly abundance therapeutic protein background to perform global HCP analysis. We provide proof of principle of this approach, which we term carrier proteome-HCP (CP-HCP) analysis, ...
ORGANISM(S): Escherichia coli Bacteria 
2026-01-12 | PXD049386 | Pride
Carrier proteome Host cell proteome E.coli 
ProteomicsDilute to Enrich for Deep Proteomics: Yolk-Depleted Carrier for a Limited Population of Embryonic (Frog) Cells
This project developed a proteomic methodology that deepens the detectable and quantifiable proteome from limited proteomes where abundant proteins pose interference. As proof-of-principle, this study used Xenopus laevis, where ~90% of the proteome is dominated by abundant yolk proteins in the early...
ORGANISM(S): Xenopus laevis (African clawed frog) 
2024-05-21 | PXD044787 | Pride
Liquid chromatography Proteomics Xenopus Ultrasensitive Mass spectrometry. Yolk 
ProteomicsA deeper look at carrier proteome effects for single-cell proteomics
We probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at h...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2022-02-24 | PXD027742 | Pride
Tmt Proteomics Single cell 
ProteomicsCarrier protein-enabled host cell proteome analysis (CP-HCP) with integrated isobaric tag interference filtering
We added increasing amounts of E coli carrier proteome to BSA, our moch recombinant protein to model interference of high-background BSA peaks with smaller peaks of E coli HCPs, using MS2 and MS3 methods to show co-fragmentation and co-elution based on similar m/z ratio. We created an interference d...
ORGANISM(S): Escherichia coli 
2026-01-12 | PXD050183 | Pride
Host cell proteins (hcps) Peptide-spectrum matches Tmt Co-elution Lc-ms Multiplexed proteomics Tryptic digest Interference Carrier proteome Data dependent acquisition Co-fragmentation 
ProteomicsCarrier protein-enabled host cell proteome analysis (CP-HCP) with integrated isobaric tag interference filtering
We used TMT labelling to set up different experiment channels containing mixtures of the host cell carrier proteome (E coli) and mock biotherapeutic (BSA), to compare with interference detection channel to model and filter interference, a phenomenon where host cell proteins (HCPs) co-elute with high...
ORGANISM(S): Escherichia coli 
2026-01-12 | PXD049970 | Pride
Boost Host cell proteins Multi-plexed proteomics Tmt Carrier proteome Lc-ms Co-isolation Interference Co-fragmentation Dda 
ProteomicsHigH-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions
Understanding how cellular proteins interact with their environment, including endogenous and exogeneous molecules, is critical for elucidating mechanisms of cellular regulation and drug action. Partial proteolysis-based techniques offer peptide-level resolution of ligand-induced conformational chan...
ORGANISM(S): Homo sapiens (Human) 
2026-09-14 | PXD077592 | Pride
Proteomics Ligand-protein interaction Partial proteolysis Lc-ms-ms 
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