Automated signature peptide approach for proteomics

Riggs, Larry; Sioma, Cathy; Regnier, Fred E.

doi:10.1016/s0021-9673(01)00900-1

Cited by 73 publications

(50 citation statements)

References 23 publications

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“…One is for the enrichment of phosphorylated peptides with Ga(III) or Fe(III) immobilized [19]. The other is for the selection of peptides with Cu(II) loaded on to the columns [20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

On-line concentration of peptides and proteins with the hyphenation of polymer monolithic immobilized metal affinity chromatography and capillary electrophoresis

Zhang

et al. 2005

Electrophoresis

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On-line concentration of peptides and proteins with the hyphenation of polymer monolithic immobilized metal affinity chromatography and capillary electrophoresisAn iminodiacetic acid (IDA)-type adsorbent is prepared at the one end of a capillary by covalently bonding IDA to the monolithic rods of macroporous poly(glycidyl methacrylate-co-ethylene dimethacrylate). Cu(II) is later introduced to the support via the interaction with IDA. By this means, polymer monolithic immobilized metal affinity chromatography (IMAC) materials are prepared. With such a column, IMAC for on-line concentration and capillary electrophoresis (CE) for the subsequent analysis are hyphenated for the analysis of peptides and proteins. The reproducibility of such a column has been proved good with relative standard deviations (RSDs) of dead time of less than 5% for injection-to-injection and 12% for column-to-column (n = 3). Through application on the analysis of standard peptides and real protein samples, such a technique has shown promising in proteome study. IntroductionCapillary electrophoresis (CE) has become a powerful separation tool and is widely used in the analysis of biomolecules, such as peptides, proteins, and polynucleotides, due to its high separation efficiency, high resolution, and fast speed [1][2][3]. However, the poor detection limit of CE caused by the short optical path length across the capillary and small injection volume is still a serious problem. Therefore, dedicated sample preparation schemes to enrich the target components before separation are usually necessary for real sample analysis. However, the commonly used procedures, such as solvent-solvent extraction and solid-phase extraction, are often laborious and time-consuming. In addition, a number of sensitive detectors, such as electrochemical detector, fluorescence detector, and mass spectrometry (MS), have also been successfully developed [4][5][6]. Nevertheless, they are sophisticated, expensive, selective, or difficult to automation compared with absorption detection.On-line concentration of sample is an alternative in CE to improve the concentration detection limits [7][8][9][10][11][12][13]. Up to now, two distinctly different methods for on-column sample enrichment have been developed, namely electrophoretic stacking [7][8][9][10][11][12][13] and chromatographic concentration [14,15]. The former one includes isotachophoresis [7], sample stacking [8,9], sweeping [10,11], and a dynamic pH junction [12,13], caused by the different electric fields applied on the sample zone and background electrolyte. In the latter one, in a capillary with stationary phase, the sample zone could be sharpened under the condition that the modified organic concentration in the mobile phase is higher than that in the sample buffer.Recently, immobilized metal affinity chromatography (IMAC) has shown great potential in the purification of proteins and peptides [16,17], and two types of IMAC columns have been applied to proteomics [18]. One is for the enrichment of phosphorylated...

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Section: Introductionmentioning

confidence: 99%

On-line concentration of peptides and proteins with the hyphenation of polymer monolithic immobilized metal affinity chromatography and capillary electrophoresis

Zhang

et al. 2005

Electrophoresis

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“…However, reaction conditions have to be chosen carefully to avoid both incomplete esterification and side reactions for instance with asparagines because they increase sample complexity and interfere with subsequent mass spectrometric analysis. Thus, various metal-ions such as Fe 31 , Ga 31 , Al 31 or Zr 41 have been used for better selectivity and phosphopeptide recovery [26,27]. Especially Ga 31 -ions have proven well [28] in different studies but Fe 31 -based methods are still used more often.…”

Section: Detection Of Phosphoproteins In 2-d Gelsmentioning

confidence: 99%

“…Especially Ga 31 -ions have proven well [28] in different studies but Fe 31 -based methods are still used more often. The good compatibility of IMAC-procedures to subsequent separation and detection techniques such as CE [29], LC-MS/MS [30,31] and direct MALDI-MS of phosphopeptides bound to IMAC-beads on the target [32], will grant this technique even wider spreading in the future. Another possibility for decreasing the co-purification of acidic peptides is the use of TiO 2 -columns [33].…”

Section: Detection Of Phosphoproteins In 2-d Gelsmentioning

confidence: 99%

State-of-the-art in phosphoproteomics

2005

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Presently, phosphorylation of proteins is the most studied and best understood PTM. However, the analysis of phosphoproteins and phosphopeptides is still one of the most challenging tasks in contemporary proteome research. Since not every phosphoprotein is accessible by a certain method and identification of the phosphorylated amino acid residue is required in the majority of cases, various strategies for the detection and localization of phosphorylations have been developed. Identification and localization of protein phosphorylations is mostly done by MS nowadays but phosphoproteins and -peptides are often suppressed in comparison to the unphosphorylated species if measured in complex mixtures. Thus, the isolation of pure phosphopeptide samples is a main task. This review gives an overview over the most frequently used methods in isolation and detection of phosphoproteins and -peptides such as specific enrichment or separation strategies as well as the localization of the phosphorylated residues by various mass spectrometric techniques.

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“…However, many techniques are used to extract or highlight peptides of choice. For example, immobilised metal ion affinity chromatography utilises chromatographic media with bound Ni ions to extract phosphopeptides from complex mixtures, thus enabling the identification of peptides from proteins involved in signalling cascades (Riggs et al 2001). Isotope-coded affinity tag (ICAT) methodologies use stable-isotope tags to differentially label two samples which can then be mixed.…”

Section: Chromatography-based Technologiesmentioning

confidence: 99%

The use of proteomic techniques to explore the holistic effects of nutrients in vivo

Griffiths

Grant

2006

Nutr. Res. Rev.

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The availability of ‘omics’ technologies is transforming scientific approaches to physiological problems from a reductionist viewpoint to that of a holistic viewpoint. This is of profound importance in nutrition, since the integration of multiple systems at the level of gene expression on the synthetic side through to metabolic enzyme activity on the degradative side combine to govern nutrient availability to tissues. Protein activity is central to the process of nutrition from the initial absorption of nutrients via uptake carriers in the gut, through to distribution and transport in the blood, metabolism by degradative enzymes in tissues and excretion through renal tubule exchange proteins. Therefore, the global profiling of the proteome, defined as the entire protein complement of the genome expressed in a particular cell or organ, or in plasma or serum at a particular time, offers the potential for identification of important biomarkers of nutritional state that respond to alterations in diet. The present review considers the published evidence of nutritional modulation of the proteome in vivo which has expanded exponentially over the last 3 years. It highlights some of the challenges faced by researchers using proteomic approaches to understand the interactions of diet with genomic and metabolic–phenotypic variables in normal populations.

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Automated signature peptide approach for proteomics

Cited by 73 publications

References 23 publications

On-line concentration of peptides and proteins with the hyphenation of polymer monolithic immobilized metal affinity chromatography and capillary electrophoresis

On-line concentration of peptides and proteins with the hyphenation of polymer monolithic immobilized metal affinity chromatography and capillary electrophoresis

State-of-the-art in phosphoproteomics

The use of proteomic techniques to explore the holistic effects of nutrients in vivo

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