ArticleProteomics2011
A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses.
Article in Proteomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Predicting response to bevacizumab in ovarian cancer: a panel of potential biomarkers informing treatment selection.Clinical cancer research : an official journal of the American Association for Cancer Research · 2013Trial
- Proteome signatures of inflammatory activated primary human peripheral blood mononuclear cells.Journal of proteomics · 2012Trial
- Protein Enrichment from Ascites Fluid Using Nanotrap Hydrogel Particle Technology.Journal of proteome research · 2026Article
- Immunoaffinity Depletion of High-Abundance Proteins from Serum/Plasma for Proteomic Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Establishing Quality Control Metrics for Large-Scale Plasma Proteomic Sample Preparation.ACS measurement science au · 2024Article
- A Carrier-Based Quantitative Proteomics Method Applied to Biomarker Discovery in Pericardial Fluid.Molecular & cellular proteomics : MCP · 2024Article
- Proteomic-based identification of APCS as candidate protein for diagnosis of patients exhibiting anti-tubercular drug induced liver injury.Scientific reports · 2023Article
- Advances in proteomics: characterization of the innate immune system after birth and during inflammation.Frontiers in immunology · 2023Review
- Advancements in automation for plasma proteomics sample preparation.Molecular omics · 2022Review
- Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database.Cancers · 2021Article
- Robust optimization of SWATH-MS workflow for human blood serum proteome analysis using a quality by design approach.Clinical proteomics · 2021Article
- Human Blood Plasma Investigation Employing 2D UPLC-UDMSMethods in molecular biology (Clifton, N.J.) · 2021Article
- Longitudinal Stroke Recovery Associated With Dysregulation of Complement System-A Proteomics Pathway Analysis.Frontiers in neurology · 2020Article
- The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.Journal of proteome research · 2017Article
- Proteomic profiling of mdx-4cv serum reveals highly elevated levels of the inflammation-induced plasma marker haptoglobin in muscular dystrophy.International journal of molecular medicine · 2017Article
- Temporal profiles of plasma proteome during childhood development.Journal of proteomics · 2017Article
- An analysis of the impact of pre-analytical factors on the urine proteome: Sample processing time, temperature, and proteolysis.Proteomics. Clinical applications · 2015Article
- Mass spectrometry-based proteomics for pre-eclampsia and preterm birth.International journal of molecular sciences · 2015Review
- Identification and Quantitation of Coding Variants and Isoforms of Pulmonary Surfactant Protein A.Journal of proteome research · 2014Article
- Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Immunodepletion of clinical fluids to overcome the dominance by a few very abundant proteins has been explored but studies are few, commonly examining only limited aspects with one analytical platform. We have systematically compared immunodepletion of 6, 14, or 20 proteins using serum from renal transplant patients, analysing reproducibility, depth of coverage, efficiency, and specificity using 2-D DIGE ('top-down') and LC-MS/MS ('bottom-up'). A progressive increase in protein number (≥2 unique peptides) was found from 159 in unfractionated serum to 301 following 20 protein depletion using a relatively high-throughput 1-D-LC-MS/MS approach, including known biomarkers and moderate-lower abundance proteins such as NGAL and cytokine/growth factor receptors. On the contrary, readout by 2-D DIGE demonstrated good reproducibility of immunodepletion, but additional proteins seen tended to be isoforms of existing proteins. Depletion of 14 or 20 proteins followed by LC-MS/MS showed excellent reproducibility of proteins detected and a significant overlap between columns. Using label-free analysis, greater run-to-run variability was seen with the Prot20 column compared with the MARS14 column (median %CVs of 30.9 versus 18.2%, respectively) and a corresponding wider precision profile for the Prot20. These results illustrate the potential of immunodepletion followed by 1-D nano-LC-LTQ Orbitrap Velos analysis in a moderate through-put biomarker discovery process.
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