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ProteomicsAssessment of sample preparation bias in mass spectrometry-based proteomics
For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-fil...
ORGANISM(S): Homo sapiens (Human) 
2018-04-06 | PXD008493 | Pride
Parotid gland Proteomics Palatine tonsils Nasal polyps Sample preparation 
ProteomicsQuantification of surfactant protein D (SPD) in human serum by liquid chromatography-mass spectrometry (LC-MS)
Quantification of intact proteins in complex biological matrices by liquid chromatography-mass spectrometry (LC-MS) is a promising analytical strategy but is technically challenging, notably for concentrations at or below the ng/mL level. Therefore, MS-based protein quantification is mostly based on...
ORGANISM(S): Homo sapiens (Human) 
2021-04-12 | PXD013415 | Pride
Biomarker Copd Lc-ms Immunoprecipitation Quantification Methionine oxidation 
ProteomicsAdsorptive microtiter plates as solid supports in affinity purification workflows
Affinity ligands such as antibodies are widely used in (bio)medical research for purifying proteins from complex biological samples. These ligands are generally immobilized onto solid supports which facilitate the separation of captured protein from sample matrix. Adsorptive microtiter plates are co...
ORGANISM(S): Murine leukemia virus isolates 
2021-11-25 | PXD027530 | Pride
Transcription factor p65 Peptidyl-prolyl cis-trans isomerase fkbp5 Immuno capture Lc-ms/ms 
ProteomicsPipelines and Systems for Threshold Avoiding Quantification of LC-MS/MS data
The accurate processing of complex LC-MS/MS data from biological samples is a major challenge for metabolomics, proteomics and related approaches. Here we present the Pipelines and Systems for Threshold Avoiding Quantification (PASTAQ) LC-MS/MS pre-processing toolset, which allows highly accurate qu...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2021-08-18 | PXD024584 | Pride
Lc-ms/ms pre-processing Isotope quantification Proteomics Label-free 
ProteomicsQuantification of the Soluble Receptor of Advanced Glycation End-Products (sRAGE) by LC-MS Without the Use of Affinity Enrichment
The study of low abundant proteins contributes to increasing our knowledge about (patho)physiological processes of ageing and disease onset and development and may lead to the identification and clinical application of disease markers. However, studying these proteins is challenging as high-abundant...
ORGANISM(S): Homo sapiens (Human) 
2019-04-09 | PXD010115 | Pride
Srage Human serum Scx fractionation Lc-ms/ms 
ProteomicsTuning Liposome Composition to Modulate the Corona Forming in Human Serum and Uptake by Cells
Nano-sized objects such as liposomes are modified by adsorption of biomolecules in biological fluids. The resulting corona critically changes nanoparticle behavior at cellular level. A better control of corona composition could allow to modulate uptake by cells. Within this context, in this work, li...
ORGANISM(S): Homo sapiens (Human) 
2020-02-28 | PXD017776 | Pride
Nanoparticle corona Human serum Liposomes Cellular uptake 
ProteomicsAssessment of sample preparation bias in mass spectrometry-based proteomics
For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-fil...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-03-13 | MSV000083561 | MassIVE
ProteomicsMALDI rat liver anticancer drug spiked-in dataset (imzML)
For the MALDI-MSI experiment, we selected 12 different drugs. The drugs were purchased from the LC Laboratories (Woburn, MA; CAS numbers: dabrafenib: 1195765-45-7, dasatinib: 302962-49-8, erlotinib: 183321-74-6, gefitinib: 184475-35-2, imatinib: 152459-95-5, lapatinib: 388082-78-8, pazopanib: 444731...
ORGANISM(S): Rattus norvegicus (Rat) 
2019-11-06 | PXD016146 | Pride
Imzml ground truth spiked-in drugs 
ProteomicsIn-situ proximity labeling of proteins associated with specific circRNA and RNA G-quadruplex
We developed a method named TAPRIP (TurboID-Assisted Proximity labeling of targeted RNA Interacting Proteins.
ORGANISM(S): Homo Sapiens 
2025-01-27 | PXD060240 |
ProteomicsCross-Platform Evaluation Reveals Sample Preparation-Driven Biological Biases despite Advances in Mass Spectrometry Performance in Serum Proteomics
Advances in mass spectrometry (MS) instrumentation and protein extraction technologies are reshaping proteomics; however, whether improved analytical performance alters the biological information accessible from different sample preparation strategies remains unclear. Here, we performed a cross-plat...
ORGANISM(S): Homo sapiens (Human) 
2026-09-11 | PXD078563 | Pride
Serum proteomics Reproducibility Quantitative accuracy Depth of proteome Orbitrap exploris 480 Bruker tims-tof ht Biomarker discovery 
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