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ProteomicsImpact of Sample Preparation Strategies on The Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics
Serum proteomics plays a crucial role in biomarker discovery and disease research, yet the selection of an optimal sample preparation method remains challenging. Evaluating the accuracy of protein quantitation is of major importance and a vital part of a benchmarking study in proteomics, since clini...
ORGANISM(S): Homo sapiens (Human) 
2025-09-15 | PXD062785 | Pride
Reproducibility Quantitative accuracy Serum proteomics Depth of coverage 
ProteomicsEvaluating Protein Enrichment Methods to Improve Biomarker Discovery in Equine Neurological Disorders
This study evaluated and compared three sample preparation strategies for proteomic analysis of equine cerebrospinal fluid (CSF): native in-solution digestion, the ProteoMiner™ Small-Capacity Enrichment Kit (Bio-Rad®), and the PreOmics Enrich-iST™ Kit (PreOmics®). CSF is in direct contact with the c...
ORGANISM(S): Equus caballus (Horse) 
2026-04-13 | PXD063239 | Pride
Cerebrospinal fluid (csf)  proteomics  native digestion  proteominer™ small-capacity enrichment kit  preomics enrich-ist™  liquid chromatography with tandem mass spectrometry (lc-ms/ms) 
ProteomicsEvaluation of the technical reproducibility of serum proteome sample preparation methods to support clinical proteomics applications
Evaluation of the efficiency and reproducibility of sample prepration methods using iST-BCT kit from PreOmics or SMART Trypsin Kit (Thermo Fisher) with in-house Rapigest protocol in human serum samples prior to mass spectrometry analysis.
ORGANISM(S): Homo sapiens (Human) 
2025-04-07 | PXD051002 | Pride
Serum  proteomics  biomarker  mass spectrometry  rapigest sf  ist-bct  smart digest trypsin 
ProteomicsComparative evaluation of different sample preparation workflows for reproducible, quantitative, and in-depth analysis of urine proteomics
The growing field of urinary proteomics has provided a promising opportunity to identify biomarkers useful for diagnosis and prognostication of a number of diseases. Urine is abundant and readily collected in a non-invasive manner which makes it eminently available for testing, however sample prepar...
ORGANISM(S): Homo sapiens (Human) 
2020-03-06 | PXD016273 | Pride
Reproducibility Urine proteomics Mass spectrometry Preomics ist Mstren Sample preparation Label-free S-trap 
ProteomicsTechnical evaluation of human plasma proteomics methods
In our study, seven plasma proteomics methods were evaluated including five MS-based protocols (Neat (Untreated), TOP14 depletion (Thermo Scientific), Enrich (PreOmics, part of Bruker now), PCA-N (Mann’s protocol + ref) and Proteograph XT (Seer)) and two antibody-based ones (Olink Target Inflammatio...
ORGANISM(S): Homo sapiens (Human) 
2025-12-16 | PXD070072 | Pride
Plasma Depletion Affinity-based proteomics Enrichment Mass spectrometry Proteomics 
UnknownImpact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics.
Not available
S-EPMC12418494 | biostudies-literature
ProteomicsEvaluation of Protein Extraction Methods to Improve Meta-Proteomics Analysis of Treated Wastewater Biofilms
Metaproteomics can be used to study functionally active biofilm-based bacterial populations in reclaimed water distribution systems, which in turn result in bacterial regrowth that impacts the water quality. However, existing protein extraction methods have differences in their protein recovery and ...
ORGANISM(S): bacterial mixed DNA library Acinetobacter junii CIP 107470 = MTCC 11364 Escherichia coli Enterococcus faecalis (Streptococcus faecalis) Staphylococcus aureus 
2023-08-04 | PXD042292 | Pride
Biofilms  metaproteomic  methods evaluation  protein extraction  treated wastewater 
ProteomicsDevelopment of a proteomic workflow for the identification of heparan sulfate proteoglycan-binding substrates of ADAM17 - Evaluation of heparin effects on sample preparation PreOmics
Ectodomain shedding, which is the proteolytic release of transmembrane proteins from the cell surface, is crucial for cell-to-cell communication and other biological processes. The metalloproteinase ADAM17 mediates ectodomain shedding of over 50 transmembrane proteins ranging from cytokines and grow...
ORGANISM(S): Mus musculus (Mouse) 
2025-05-07 | PXD055002 | Pride
Sheddome Adam17 Ectodomain shedding Heparin Disintegrin metalloproteinases Secretome 
ProteomicsComparative analysis of MS sample preparation methods
We compare the most commonly used proteomic sample preparation strategies such as classical in solution digest protocols, SPEED, FASP, STrap, SP3, as well as the commercially available kits iST (PreOmics) and EasyPep (Thermo Scientific) in their efficacy to extract proteomes from HeLa cells. We find...
ORGANISM(S): Homo sapiens (Human) 
2022-09-06 | PXD030406 | Pride
Hela Human Sample preparation Lc-ms/ms 
ProteomicsCathepsin S in Mycobacterium avium subsp. paratuberculosis Infected Dairy Cows
In this study, samples of 16 dairy cows from a MAP infected farm were used. Serum, milk and fecal samples were collected. Categorizing these cows into two groups based on their MAP infection status different standard methods for detection MAP were applied. Healthy controls showed no positive results...
ORGANISM(S): Bos taurus (Bovine) 
2024-06-22 | PXD048042 | Pride
Preomics Serum Label-free mass spectrometry 
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