Impact of Replicate Types on Proteomic Expression Analysis

Karp, Natasha A.; Spencer, Matthew; Lindsay, Helen; O’Dell, Kevin; Lilley, Kathryn S.

doi:10.1021/pr050084g

Cited by 145 publications

(152 citation statements)

References 23 publications

(46 reference statements)

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“…2001; Karp et al. 2005), with the “genotype” being a generic term for the three populations (JJ, TT and VV). ANOVA results are shown in Table 1 and both the “genotype” and “spot” were significant ( P < 0.05).…”

Section: Resultsmentioning

confidence: 99%

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Protein changes in abalone foot muscle from three geographical populations of Haliotis diversicolor based on proteomic approach

Miao

et al. 2016

Ecology and Evolution

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Using two‐dimensional gel electrophoresis, the foot muscle proteome of three geographical populations of Haliotis diversicolor were examined, with a total of 922 ± 21 protein spots detected in the Japanese population (JJ), 904 ± 25.6 in the Taiwanese population (TT), and 936 ± 16.2 in the Vietnamese population (VV). Of these, 254 spots showed differential expression and 85 protein spots percentage volumes varied more than twofold. Both “genotype” and “spot” analysis of variance approaches significantly showed differences among the three populations. Hierarchical clustering analysis showed that TT and VV clustered together followed by clustering with JJ, which is consistent with their geographical location. Following matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry, 30 differentially expressed proteins involved in major biological processes including energy production and storage and stress response were identified. Of these proteins, proteins pertaining to muscle contraction and muscle protein regulation showed highest expression levels in VV samples. Proteins involved in energy production and storage, including ATP synthase beta subunit, fructose‐1,6‐bisphosphate aldolase, arginine kinase, enolase, triosephosphate isomerase, and tauropine dehydrogenase, showed diverse expression patterns among the three populations. For stress‐responsive proteins, the expression of heat shock protein 70 was JJ > VV > TT. The expression pattern of Cu/Zn‐superoxide dismutase was JJ > VV > TT. Overall, these results may aid in the detection of new differentially expressed proteins within three different abalone populations.

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Section: Resultsmentioning

confidence: 99%

“…As previous described (Karp et al. 2005), only spots presented in all three technical replicates were analyzed (Diz and Skibinski 2007). To compare the three populations, a two‐sided analysis of variance (ANOVA) was used, to include “spot” and “genotype” factors (Di et al.…”

Section: Methodsmentioning

confidence: 99%

Protein changes in abalone foot muscle from three geographical populations of Haliotis diversicolor based on proteomic approach

Miao

et al. 2016

Ecology and Evolution

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“…Such issues have only recently begun to be addressed in a serious fashion (see eg. [Hu et al, 2005], [Karp et al, 2005], [Wagner et al, 2004], [Vitzthum et al, 2005], [West-Nielsen et al, 2005]). It also seems in some sense wasteful to capture a complete proteomic spectrum containing potentially thousands of components when only a handful of known components will ultimately be used for diagnosis.…”

Section: Overviewmentioning

confidence: 99%

Mining whole-sample mass spectrometry proteomics data for biomarkers – An overview

McDonald

Skipp

Bennell

et al. 2009

Expert Systems with Applications

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In this paper we aim to provide a concise overview of designing and conducting an MS proteomics experiment in such a way as to allow statistical analysis that may lead to the discovery of novel biomarkers. We provide a summary of the various stages that make up such an experiment, highlighting the need for experimental goals to be decided upon in advance. We discuss issues in experimental design at the sample collection stage, and good practise for standardising protocols within the proteomics laboratory. We then describe approaches to the data mining stage of the experiment, including the processing steps that transform a raw mass spectrum into a useable form. We propose a permutation-based procedure for determining the significance of reported error rates. Finally, because of its general advantages in speed and cost, we suggest that MS proteomics may be a good candidate for an early primary screening approach to disease diagnosis, identifying areas of risk and making referrals for more specific tests without necessarily making a diagnosis in its own right. Our discussion is illustrated with examples drawn from experiments on bovine blood serum conducted in the Centre for Proteomic Research (CPR) at Southampton University.

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“…Proteomics: Protein was extracted from 12 adult male Drosophila aged between 1 and 2 days using protocols and statistical analyses described previously (Karp et al 2005). Protein concentration was determined at the Cambridge Centre for Proteomics (CCP) using the BioRad DC protein assay (Bio-Rad).…”

Section: Ey01983mentioning

confidence: 99%

“…Standardized abundance was calculated by dividing spot volumes by the Cy2 internal standard for each spot. Statistical analysis was applied using standard ANOVA (Karp et al 2005). Spots with P , 0.05 for random occurrence were considered to differ significantly between samples.…”

Section: Ey01983mentioning

confidence: 99%

The Dominant Cold-SensitiveOut-ColdMutants ofDrosophila melanogasterHave Novel Missense Mutations in the Voltage-Gated Sodium Channel Geneparalytic

et al. 2008

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Here we report the molecular characterization of Out-cold (Ocd) mutants of Drosophila melanogaster, which produce a dominant, X-linked, cold-sensitive paralytic phenotype. From its initial 1.5-Mb cytological location within 13F1-16A2, P-element and SNP mapping reduced the Ocd critical region to ,100 kb and to six candidate genes: hangover, CG9947, CG4420, eIF2a, Rbp2, and paralytic (para). Complementation testing with para null mutations strongly suggests Ocd and para are allelic, as does gene rescue of Ocd semilethality with a wild-type para transgene. Pesticide resistance and electrophysiological phenotypes of Ocd mutants support this conclusion. The para gene encodes a voltage-gated sodium channel. Sequencing the Ocd lines revealed mutations within highly conserved regions of the para coding sequence, in the transmembrane segment S6 of domain III (I1545M and T1551I), and in the linker between domains III and IV (G1571R), the location of the channel inactivation gate. The G1571R mutation is of particular interest as mutations of the orthologous residue (G1306) in the human skeletal muscle sodium channel gene SCN4A are associated with cases of periodic paralysis and myotonia, including the human cold-sensitive disorder paramyotonia congenita. The mechanisms by which sodium channel mutations cause cold sensitivity are not well understood. Therefore, in the absence of suitable vertebrate models, Ocd provides a system in which genetic, molecular, physiological, and behavioral tools can be exploited to determine mechanisms underlying sodium channel periodic paralyses. T HE molecular mechanisms underlying cold sensitivity in metazoans are not well understood, not least because relatively few studies have addressed this question. A few cold-sensitive mutations have been described in Drosophila melanogaster (Siddiqi and Benzer 1976;Sondergaard 1980;Lilly et al. 1994), but again the precise mechanisms by which these specific mutations lead to cold sensitivity have not been elucidated. The objective of this study was to identify the biological processes underlying cold sensitivity.The dominant cold-sensitive paralytic Out-cold (Ocd) mutations of D. melanogaster were originally isolated in a screen for X-linked male-lethal mutations (Sondergaard 1975(Sondergaard , 1979. Further analyses of the male-lethal stocks identified seven lines in which heterozygous mutant females exhibited a dominant cold-sensitive paralysis.

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Impact of Replicate Types on Proteomic Expression Analysis

Cited by 145 publications

References 23 publications

Protein changes in abalone foot muscle from three geographical populations of Haliotis diversicolor based on proteomic approach

Protein changes in abalone foot muscle from three geographical populations of Haliotis diversicolor based on proteomic approach

Mining whole-sample mass spectrometry proteomics data for biomarkers – An overview

The Dominant Cold-SensitiveOut-ColdMutants ofDrosophila melanogasterHave Novel Missense Mutations in the Voltage-Gated Sodium Channel Geneparalytic

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