Tagless extraction-retentate chromatography: A new global protein digestion strategy for monitoring differential protein expression

Weinberger, Scot R.; Viner, Rosa; Ho, Patrick A.

doi:10.1002/1522-2683(200209)23:18<3182::aid-elps3182>3.0.co;2-5

Cited by 41 publications

(20 citation statements)

References 29 publications

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“…Another strategy for monitoring differential protein expression and identifying low-abundance proteins was introduced by Weinberger et al (309). In this approach, proteins of E. coli lysates were digested, and the resultant peptides were selectively extracted by covalent attachment of methionine residues with bromoacetyl-reactive groups tethered to the surface of glass beads packed in small reaction vessels.…”

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

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“…In future work, however, replacement of 2 H with 13 C within the "heavy" derivatization reagent will ensure that light and heavy isotopic variants coelute upon HPLC fractionation, thereby allowing more accurate quantitation without the need for signal averaging across an entire chromatographic peak. For future applications involving the analysis of methionine sulfonium ion containing peptides from complex biologically derived mixtures, the fixed charge derivatives could be pre-enriched by a range of methods prior to mass spectrometry analysis, including diagonal chromatography [102], strong cation exchange [76,103], or solid phase capture [77], thereby simplifying the mixture complexity and minimizing the potential for m/z overlap between unlabeled and labeled peptide ions. However, either of the two later approaches is preferred because of the ability to obtain direct enrichment of labeled peptides without requirement for separate chromatographic analysis of both unmodified and modified samples.…”

Section: Differential Quantitative Analysis By Neutral Loss Scan Modementioning

confidence: 99%

Selective identification and quantitative analysis of methionine containing peptides by charge derivatization and tandem mass spectrometry

Reid

Roberts

Simpson

et al. 2005

J. Am. Soc. Mass Spectrom.

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To enable the development of a tandem mass spectrometry (MS/MS) based methodology for selective protein identification and differential quantitative analysis, a novel derivatization strategy is proposed, based on the formation of a "fixed-charge" sulfonium ion on the side-chain of a methionine amino acid residue contained within a protein or peptide of interest. The gas-phase fragmentation behavior of these side chain fixed charge sulfonium ion containing peptides is observed to result in exclusive loss of the derivatized side chain and the formation of a single characteristic product ion, independently of charge state or amino acid composition. Thus, fixed charge containing peptide ions may be selectively identified from complex mixtures, for example, by selective neutral loss scan mode MS/MS methods. Further structural interrogation of identified peptide ions may be achieved by subjecting the characteristic MS/MS product ion to multistage MS/MS (MS3) in a quadrupole ion trap mass spectrometer, or by energy resolved "pseudo" MS3 in a triple quadrupole mass spectrometer. The general principles underlying this fixed charge derivatization approach are demonstrated here by MS/MS, MS3 and "pseudo" MS3 analysis of side chain fixed-charge sulfonium ion derivatives of peptides containing methionine formed by reaction with phenacylbromide. Incorporation of "light" and "heavy" isotopically encoded labels into the fixed-charge derivatives facilitates the application of this method to the quantitative analysis of differential protein expression, via measurement of the relative abundances of the neutral loss product ions generated by dissociation of the light and heavy labeled peptide ions. This approach, termed "selective extraction of labeled entities by charge derivatization and tandem mass spectrometry" (SELECT), thereby offers the potential for significantly improved sensitivity and selectivity for the identification and quantitative analysis of peptides or proteins containing selected structural features, without requirement for extensive fractionation or otherwise enrichment from a complex mixture prior to analysis.

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“…Next-generation instruments using ProteinChip s tandem MS techniques are being developed and should greatly improve the ability to identify proteins directly. 49 Petricoin et al 50 recently published the results of a landmark study in which they identified a proteomic pattern in serum that is diagnostic for ovarian cancer. Using the ProteinChip s /SELDI technology and a custom algorithm to recognize protein patterns in the spectra, they first used sera from 50 unaffected women and 50 patients with ovarian cancer to identify a proteomic pattern that completely discriminated cancer from noncancer.…”

Section: Lc/ms Methods and Icatmentioning

confidence: 99%

Pharmacoproteomics in drug development

Witzmann

Grant

2003

Pharmacogenomics J

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The field of proteomics is taking on increased significance as the relevance of investigating and understanding protein expression in disease and drug development is appreciated. Recent advances in proteomics have been driven by the availability of numerous annotated whole-genome sequences and a broad range of technological and bioinformatic developments that underscore the complexity of the proteome. This review briefly addresses some of the various technologies that comprise Expression Proteomics and Functional Proteomics, citing examples where these emerging approaches have been applied to pharmacology, toxicology, and the development of drugs.

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Tagless extraction-retentate chromatography: A new global protein digestion strategy for monitoring differential protein expression

Cited by 41 publications

References 29 publications

TheEscherichia coliProteome: Past, Present, and Future Prospects

TheEscherichia coliProteome: Past, Present, and Future Prospects

Selective identification and quantitative analysis of methionine containing peptides by charge derivatization and tandem mass spectrometry

Pharmacoproteomics in drug development

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