Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates

Wang, Shihong; Zhang, Xiang; Regnier, Fred E.

doi:10.1016/s0021-9673(01)01509-6

Cited by 103 publications

(92 citation statements)

References 31 publications

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“…For quantitative comparison, two samples may be labeled with stable isotopes prior to sample separation, either by metabolic incorporation or through chemical derivatization. In this way, proteins derived from the different samples (e.g., normal versus abnormal or untreated versus treated samples) can be directly separated, identified, and quantified using n-D LC-MS/MS (36,303,305). A recently developed, attractive method for quantitative comparison of two proteomes is the isotope-coded affinity tag (ICAT) method (331).…”

Section: Vol 70 2006mentioning

confidence: 99%

TheEscherichia coliProteome: Past, Present, and Future Prospects

Han¹,

Lee

2006

Microbiol Mol Biol Rev

162

130

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SUMMARY Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects.

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Section: Vol 70 2006mentioning

confidence: 99%

TheEscherichia coliProteome: Past, Present, and Future Prospects

Han¹,

Lee

2006

Microbiol Mol Biol Rev

162

130

View full text Add to dashboard Cite

show abstract

“…In turn, when the peptides from the two populations labeled with the light/heavy isotope, and mixed in a 1:1 ratio, were analyzed by MS, the relative peaks will be shifted by 3 mass units, for the singly labeled, or by 6 mass units (for the doubly labeled), having an area ratio that is proportional to their relative abundance in the two sample specimens. In a second approach, the same group adopted acylation of peptides via light and heavy (deuterated) succinic anhydride (Wang & Regnier, 2001;Wang et al, 2002). Here too, a few peptides that were differentially labeled and that terminated with an Arg will exhibit monoisotopic peaks that are spaced apart by 4 a.m.u., whereas those having a Lys at their C-terminus will exhibit a difference of 8 a.m.u.…”

Section: Global Internal Standard Strategy (Gist)mentioning

confidence: 99%

Modern strategies for protein quantification in proteome analysis: Advantages and limitations

Hamdan

Righetti

2002

Mass Spectrometry Reviews

130

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Over the last 3 years, a number of mass spectrometry-based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two-step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy-isotope-labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi-protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses.

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“…Peptide mapping and sequencing of proteins require as complete as possible fragmentation of the protein in a short time, resulting in well-defined and reproducible peptide patterns [1][2][3][4]. Regardless of the separation method, the resulting peaks profile provides for each protein a unique fingerprint for each protein called a "peptide map" [5]. efficient MS analysis.…”

Section: Introductionmentioning

confidence: 99%

Functionalized magnetic micro‐ and nanoparticles: Optimization and application to μ‐chip tryptic digestion

et al. 2006

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The preparation of an easily replaceable protease microreactor for micro-chip application is described. Magnetic particles coated with poly(N-isopropylacrylamide), polystyrene, poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate), poly(glycidyl methacrylate), [(2-amino-ethyl)hydroxymethylen]biphosphonic acid, or alginic acid with immobilized trypsin were utilized for heterogeneous digestion. The properties were optimized, with the constraint of allowing immobilization in a microchannel by a magnetic field gradient. To obtain the highest digestion efficiency, sub-micrometer spheres were organized by an inhomogeneous external magnetic field perpendicularly to the direction of the channel. Kinetic parameters of the enzyme reactor immobilized in micro-chip capillary (micro-chip immobilized magnetic enzyme reactor (IMER)) were determined. The capability of the proteolytic reactor was demonstrated by five model (glyco)proteins ranging in molecular mass from 4.3 to 150 kDa. Digestion efficiency of proteins in various conformations was investigated using SDS-PAGE, HPCE, RP-HPLC, and MS. The compatibility of the micro-chip IMER system with total and limited proteolysis of high-molecular-weight (glyco)proteins was confirmed. It opens the route to automated, high-throughput proteomic micro-chip devices.

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Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates

Cited by 103 publications

References 31 publications

TheEscherichia coliProteome: Past, Present, and Future Prospects

TheEscherichia coliProteome: Past, Present, and Future Prospects

Modern strategies for protein quantification in proteome analysis: Advantages and limitations

Functionalized magnetic micro‐ and nanoparticles: Optimization and application to μ‐chip tryptic digestion

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