Principal component analysis of mass spectra of peptides generated from the tryptic digestion of protein mixtures

Bryant, Duncan; Monté, Soraya; Man, Wai J.; Kramer, Kerstin; Bugelski, Peter J.; Neville, William A.; White, Ian R.; Camilleri, Patrick

doi:10.1002/rcm.247

Cited by 17 publications

(9 citation statements)

References 20 publications

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“…Analytical quantities (50-100 mg) of liver tissue were used to prepare lysates as described by Bryant et al [3]. Aliquots were added to 7 volumes of IPG sample buffer (7 M urea, 2 M thiourea, 4% w/v CHAPS, 20 mM DTT) and to 1 volume of 26reducing SDS-PAGE sample buffer (125 mM Tris-HCl pH 6.8, 4% w/v SDS, 100 mM DTT, 20% w/v sucrose).…”

Section: Sample Preparation and Gel Electrophoresismentioning

confidence: 99%

“…In instances where MALDI-TOF MS peptide mapping did not yield an unambiguous protein identification for trypsin digested 2-D gel spots, NanoESI-MS using a Micromass Q-Tof was used as described by Bryant et al [3]. The main advantage of nanoESI over MALDI-TOF MS is that amino acid sequence and mass data can be obtained from peptide mixtures which can then be used for more stringent searching of nonredundant protein databases.…”

Section: Nanoesi-msmentioning

confidence: 99%

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Protein expression analysis of drug-mediated hepatotoxicity in the Sprague-Dawley rat

Man¹,

White²,

Bryant³

et al. 2002

Proteomics

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This study has investigated the protein changes in rat liver elicited by a group of model hepatotoxicants, methapyrilene, cyproterone acetate and dexamethasone and offers a compelling argument in support of the use of two-dimensional polyacrylamide gel electrophoresis and mass spectrometry for the identification of compound specific biomarkers. The different treatments caused distinct changes to the rat liver proteome. Many of the protein changes could be associated with the known pharmacological and toxicological mechanisms of action of these drugs, whereas for other proteins, the rationale behind the alterations was less obvious. Furthermore, these changes can be used to classify the treatments with a view to utilising them as 'molecular signatures' to further our understanding of less well studied drugs such as SKF-106686 (an adrenoreceptor agonist). This approach has the potential for opening up new avenues for the exploration of molecular mechanisms of toxicity. This paper has explored the feasibility of proteomics to provide valuable information on the biochemical consequences elicited by hepatototoxic drugs.

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Section: Sample Preparation and Gel Electrophoresismentioning

confidence: 99%

Section: Nanoesi-msmentioning

confidence: 99%

Protein expression analysis of drug-mediated hepatotoxicity in the Sprague-Dawley rat

Man¹,

White²,

Bryant³

et al. 2002

Proteomics

Self Cite

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“…Through different database searching algorithms, some high accuracy peptide masses can also be applied to identify individual proteins in complex protein mixtures 9,. 10 Obviously, avoiding 2D‐PAGE would enormously increase throughput of protein identification as well.…”

mentioning

confidence: 99%

High accuracy mass measurement of peptides with internal calibration using a dual electrospray ionization sprayer system for protein identification

Zhou

Wang

et al. 2002

Rapid Comm Mass Spectrometry

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A dual-ESI-sprayer system was constructed and applied to achieve high accuracy of peptide mass measurement for protein identification by means of peptide mapping. Sample was introduced in one sprayer, and reference in the other, thus making internal calibration possible greatly enhancing the mass accuracy. Several samples were utilized to evaluate the reliability of this dual-ESI-sprayer system. The range of mass errors was 0.16-5.37 ppm. The peptide masses of tryptic digests of myoglobin (horse) were measured by the HPLC/dual-ESI-MS system, with mass deviations ranging from 0.01-7.67 ppm, and about 75% mass deviations below 5 ppm with 40% below 1[?]ppm. These peptide masses were utilized to perform database searching for protein identification, and compared to results obtained by external calibration. This comparison showed that the internal calibration provides a more reliable method of protein identification, with a much smaller number of required peptides for matching, and with less CPU time consumed for database searching.

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“…Chemometrics designates the handling of multivariate chemical data31 and the technique applies to scientists who want to obtain valuable information from complex datasets 32. Among the techniques available principal component analysis (PCA) is one of the most widely used 33. This study has the purpose to implement the chemometric tools PCA and interval partial least squares (iPLS)29 to MALDI‐TOFMS data.…”

mentioning

confidence: 99%

Determination of wheat quality by mass spectrometry and multivariate data analysis

Gottlieb¹,

Schultz²,

Petersen³

et al. 2002

Rapid Comm Mass Spectrometry

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Multivariate analysis has been applied as support to proteome analysis in order to implement an easier and faster way of data handling based on separation by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The characterisation phase in proteome analysis by means of simple visual inspection is a demanding process and also insecure because subjectivity is the controlling element. Multivariate analysis offers, to a considerable extent, objectivity and must therefore be regarded as a neutral way to evaluate results obtained by proteome analysis. Proteome analysis of storage proteins from the wheat gluten complex based on two-dimensional electrophoresis and analysis of the N-terminal sequence has revealed a protein homologous to gamma-gliadins, tentatively associated with quality and within the molecular weight range 27-35 kDa. Further examinations of gliadin data based on mass spectrometry revealed that quality among wheat varieties could be determined by means of principal component analysis. Further examinations by interval partial least squares made it possible to encircle an overall optimal molecular weight interval from 31.5 to 33.7 kDa. The use of multivariate analysis on data from mass spectrometry has thus shown to be a promising technique to minimize the number of two-dimensional gels within the field of proteome analysis.

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Principal component analysis of mass spectra of peptides generated from the tryptic digestion of protein mixtures

Cited by 17 publications

References 20 publications

Protein expression analysis of drug-mediated hepatotoxicity in the Sprague-Dawley rat

Protein expression analysis of drug-mediated hepatotoxicity in the Sprague-Dawley rat

High accuracy mass measurement of peptides with internal calibration using a dual electrospray ionization sprayer system for protein identification

Determination of wheat quality by mass spectrometry and multivariate data analysis

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