Sequential depletion of human serum for the search of osteoarthritis biomarkers

Fernández-Costa, Carolina; Calamia, V.; Fernández-Puente, Patricia; Capelo-Martínez, José-Luis; Ruiz-Romero, Cristina; Blanco, Francisco J.

doi:10.1186/1477-5956-10-55

Cited by 37 publications

(21 citation statements)

References 33 publications

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“…The reduction of complexity can be performed by classical methods such as organic solvent solubilization and precipitation methods and by immuno depletion methods [3, 4]. …”

Section: Methodologies Used To Reduce the Complexity Of Proteomic Smentioning

confidence: 99%

“…The depletion of these HAPs allows the identification of low abundance proteins (LAPs) in proteomic analysis as well as the discovery of new biomarkers for diseases. The organic precipitation methods have been developed to reduce sample complexity by depletion of these HAPs in plasma using organic solvents such as acetonitrile, acetone, and trichloroacetic acid (TCA) [3, 4, 11-13]. …”

Section: Methodologies Used To Reduce the Complexity Of Proteomic Smentioning

confidence: 99%

“…In another study, the combination of a chemical sequential depletion method based on two protein precipitations with acetonitrile and dithiothreitol (DTT) have been reported for reducing HAPs in osteoarthritis diseased serum [4]. The two chemical depletions were combined in a sequential way in order to efficiently reduce the dynamic range of proteins in the sample.…”

Section: Methodologies Used To Reduce the Complexity Of Proteomic Smentioning

confidence: 99%

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Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in‐depth proteomics analysis—An update covering the period 2011–2014

2014

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This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As the previous review article, the present one is concerned with proteomic sample preparation (e.g., depletion of high abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular sub-proteome), and the subsequent chromatographic and/or electrophoretic pre-fractionation prior to peptide separation and identification by LC-MS/MS. This review article is distinguished from its second version published in Electrophoresis 2012, 33, 74-88 by expanding on capturing/enriching sub-phosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid 2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field.

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“…The reduction of complexity can be performed by classical methods such as organic solvent solubilization and precipitation methods and by immuno depletion methods [3, 4]. …”

Section: Methodologies Used To Reduce the Complexity Of Proteomic Smentioning

confidence: 99%

Section: Methodologies Used To Reduce the Complexity Of Proteomic Smentioning

confidence: 99%

Section: Methodologies Used To Reduce the Complexity Of Proteomic Smentioning

confidence: 99%

See 1 more Smart Citation

Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in‐depth proteomics analysis—An update covering the period 2011–2014

2014

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“…Widely used methods, such as immunodepletion for reducing the highly abundant proteins, have been applied; novel strategies are still developing. A recent study reported a method for pre-processing human serum samples based on a chemical depletion method involving two sequential protein precipitation steps with acetonitrile and DTT, with a subsequent two-dimensional difference gel electrophoresis (2D-DIGE) analysis and MALDI-TOF/TOF analysis to identify OA biomarkers (Fernandez-Costa et al, 2012). Reproducibility was examined by technical and biological replicates.…”

Section: Proteomic Analysis Of Serum In Oamentioning

confidence: 99%

Biomarkers and proteomic analysis of osteoarthritis

2014

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Our friend and colleague, Dr. Dick Heinegård, contributed greatly to the understanding of joint tissue biochemistry, the discovery and validation of arthritis-related biomarkers and the establishment of methodology for proteomic studies in osteoarthritis (OA). To date, discovery of OA-related biomarkers has focused on cartilage, synovial fluid and serum. Methods, such as affinity depletion and hyaluronidase treatment have facilitated proteomics discovery research from these sources. Osteoarthritis usually involves multiple joints; this characteristic makes it easier to detect OA with a systemic biomarker but makes it hard to delineate abnormalities of individual affected joints. Although the abundance of cartilage proteins in urine may generally be lower than other tissue/sample sources, the protein composition of urine is much less complex and its collection is non-invasive thereby facilitating the development of patient friendly biomarkers. To date however, relatively few proteomics studies have been conducted in OA urine. Proteomics strategies have identified many proteins that may relate to pathological mechanisms of OA. Further targeted approaches to validate the role of these proteins in OA are needed. Herein we summarize recent proteomic studies related to joint tissues and the cohorts used; a clear understanding of the cohorts is important for this work as we expect that the decisive discoveries of OA-related biomarkers rely on comprehensive phenotyping of healthy non-OA and OA subjects. Besides the common phenotyping criteria that include, gender, age, and body mass index (BMI), it is essential to collect data on symptoms and signs of OA outside the index joints and to bolster this with objective imaging data whenever possible to gain the most precise appreciation of the total burden of disease. Proteomic studies on systemic biospecimens, such as serum and urine, rely on comprehensive phenotyping data to unravel the true meaning of the proteomic results.

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“…The IAC approaches have been routinely coupled with both global discovery and targeted verification for disease-biomarker related studies [114, 128], and the applications include pancreatic cancer [124], ovarian cancer [129, 130], breast cancer [131, 132], renal cancer [133], gastric cancer [134], prostate cancer [135, 136], osteoarthritis [137–139], cardiovascular disease [120, 140], etc .…”

Section: Proteomic Applications Of Iac In Biofluidsmentioning

confidence: 99%

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids

Duan

Liu

et al. 2016

Journal of Chromatography B

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Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.

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Sequential depletion of human serum for the search of osteoarthritis biomarkers

Cited by 37 publications

References 33 publications

Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in‐depth proteomics analysis—An update covering the period 2011–2014

Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in‐depth proteomics analysis—An update covering the period 2011–2014

Biomarkers and proteomic analysis of osteoarthritis

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids

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