Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis

Bock, Muriel De; Seny, Dominique de; Meuwis, Marie‐Alice; Servais, Anne-Catherine; Minh, Tran Quang; Closset, Jean; Chapelle, Jean-Paul; Louis, Édouard; Malaise, Michel; Merville, Marie‐Paule; Fillet, Marianne

doi:10.1016/j.talanta.2010.04.029

Cited by 37 publications

(24 citation statements)

References 46 publications

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“…endoproteinase Lys-C, OmpT outer membrane protease) cutting the proteins less frequently than trypsin, thus producing longer peptides that allows comprehensive characterization of large proteins along with their posttranslational modifications [31,32]. These three approaches are compared in Comprehensive analysis of plasma proteins is a challenging task due to the high complexity and large dynamic range of the plasma components, thus appropriate sample preparation, such as pre-fractionation is highly advised before the deeper exploration of its proteome for biomarker discovery [33]. The usual workflow of sample preparation for MS or MS/MS-based proteomics analysis starts with the depletion of high abundance proteins that can interfere with the detection of the lower abundant ones.…”

Section: Plasma Fractionation For Proteomicsmentioning

confidence: 99%

Medicinal Chemistry Meets Proteomics: Fractionation of the Human Plasma Proteome

Kovács¹,

Guttman²

2013

CMC

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Human plasma and its fractions/derivatives are frequently used materials in biomedicine as it contains thousands and thousands of proteins representing the majority of human proteome. Several important methods were developed in the past for the fractionation of this important biological fluid and their use for medicinal purposes. One of the greatest challenges is the very large dynamic range of plasma proteins ranging up to 10-12 orders of magnitude. Early attempts were mainly based on methods such as salting out or cold ethanol precipitation, as well as chromatography utilizing affinity, size exclusion, ion exchange and hydrophobic interaction techniques. More recently, fractionation applications started with the depletion of the high abundant plasma components, such as serum albumin and immunoglobulins, before isolating lower abundant proteins of interest. Plasma volumes were utilized from the milliliter scale for diagnostic applications to hundreds of liters for industrial scale plasma fractionation (e.g., medicinal product manufacturing). In this paper we review this important part of medicinal chemistry, highlighting the traditional methods along with some of their variations as well as the most significant recent achievements of the field.

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Section: Plasma Fractionation For Proteomicsmentioning

confidence: 99%

Medicinal Chemistry Meets Proteomics: Fractionation of the Human Plasma Proteome

Kovács¹,

Guttman²

2013

CMC

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“…Comprehensive comparisons of peptideextraction methods have been made mainly in terms of the number of identified peptides [19,[25][26][27][28]. However, to obtain a complete understanding of different extraction methods, it was necessary to investigate the recoveries of peptides with different properties after treatment by different extraction methods.…”

Section: Introductionmentioning

confidence: 99%

Quantitative evaluation of peptide-extraction methods by HPLC–triple-quad MS–MS

et al. 2014

Anal Bioanal Chem

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In this study, the efficiency of five peptide-extraction methods—acetonitrile (ACN) precipitation, ultrafiltration, C18 solid-phase extraction (SPE), dispersed SPE with mesoporous carbon CMK-3, and mesoporous silica MCM-41—was quantitatively investigated. With 28 tryptic peptides as target analytes, these methods were evaluated on the basis of recovery and reproducibility by using high-performance liquid chromatography-triple-quad tandem mass spectrometry in selected-reaction-monitoring mode. Because of the distinct extraction mechanisms of the methods, their preferences for extracting peptides of different properties were revealed to be quite different, usually depending on the pI values or hydrophobicity of peptides. When target peptides were spiked in bovine serum albumin (BSA) solution, the extraction efficiency of all the methods except ACN precipitation changed significantly. The binding of BSA with target peptides and nonspecific adsorption on adsorbents were believed to be the ways through which BSA affected the extraction behavior. When spiked in plasma, the performance of all five methods deteriorated substantially, with the number of peptides having recoveries exceeding 70% being 15 for ACN precipitation, and none for the other methods. Finally, the methods were evaluated in terms of the number of identified peptides for extraction of endogenous plasma peptides. Only ultrafiltration and CMK-3 dispersed SPE performed differently from the quantitative results with target peptides, and the wider distribution of the properties of endogenous peptides was believed to be the main reason.

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“…The results also confirmed that the on-chip sample fractionation integrated with microfluidic channels provided superior reproducibility and demonstrated the reliability of our MPS chips in the pretreatment of complex biological samples compared to other methods reported in the literature. 35 As this approach evolves along with contemporary proteomic isolation and iden-tification techniques, systems-mediated identification of disease-specific protein signatures may soon play a large role in the selection of personalized therapeutics, specifically pertaining to the real-time assessment of efficacy and toxicity, and in the rational modulation of therapy based on changes in the proteome associated with the prognosis of the disease.…”

mentioning

confidence: 99%

Microfluidic enrichment of small proteins from complex biological mixture on nanoporous silica chip

Gopal

Lin

et al. 2011

Biomicrofluidics

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The growing field of miniaturized diagnostics is hindered by a lack of pre-analysis treatments that are capable of processing small sample volumes for the detection of low concentration analytes in a high-throughput manner. This letter presents a novel, highly efficient method for the extraction of low-molecular weight ͑LMW͒ proteins from biological fluids, represented by a mixture of standard proteins, using integrated microfluidic systems. We bound a polydimethylsiloxane layer patterned with a microfluidic channel onto a well-defined nanoporous silica substrate. Using rapid, pressure-driven fractionation steps, this system utilizes the size-exclusion properties of the silica nanopores to remove high molecular weight proteins while simultaneously isolating and enriching LMW proteins present in the biological sample. The introduction of the microfluidic component offers important advantages such as high reproducibility, a simple user interface, controlled environment, the ability to process small sample volumes, and precise quantification. This solution streamlines high-throughput proteomics research on many fronts and may find broad acceptance and application in clinical diagnostics and point of care detection. © 2011 American Institute of Physics. ͓doi:10.1063/1.3528237͔Despite advances in the analysis of blood metabolites, the histochemical evaluation of tissue biopsies, and improvements in imaging approaches, early detection and diagnosis of human disease still suffers from severe limitations. A promising strategy to overcome this conundrum is the detection of molecular signatures from readily available body fluids. 1 However, the onset of most diseases cannot be unequivocally identified on the basis of a single biomarker. 2-4 Considerable attention has been devoted to the development of proteomic methods for the simultaneous, quantitative detection of multiple protein and peptide biomarkers ͑signature profiles͒ using mass spectrometry ͑MS͒. 5-7 A critical aspect of the development of MS-based proteomics and peptidomics is the extraordinarily broad assortment of molecular species in blood, with concentrations ranging over more than ten orders of magnitude. 8 This dynamic complexity is a significant barrier to the detection of disease-related peptides, many of which are present in trace amounts and are hidden within a background of highly abundant, nonrelevant proteins. Several strategies for sample treatment prior to MS analysis have been developed to address these limitations, 9,10 including conventional two-dimensional gel electrophoresis, 11 prefractionation processes, 12,13 depletion of highabundance proteins, 14,15 coated magnetic bead-based extractions, 16 and beads equalization. 17,18 Despite these substantial advances, many of the listed techniques are prone to experimental variability, limited reproducibility, unwieldy handling procedures, protein instability during sample a͒ These authors contributed equally to this work.

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Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis

Cited by 37 publications

References 46 publications

Medicinal Chemistry Meets Proteomics: Fractionation of the Human Plasma Proteome

Medicinal Chemistry Meets Proteomics: Fractionation of the Human Plasma Proteome

Quantitative evaluation of peptide-extraction methods by HPLC–triple-quad MS–MS

Microfluidic enrichment of small proteins from complex biological mixture on nanoporous silica chip

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