Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

Godoy, Lyris Martins Franco de; Olsen, Jesper V.; Cox, Jürgen; Nielsen, Michael L.; Hubner, Nina C.; Fröhlich, Florian; Walther, Tobias C.; Mann, Matthias

doi:10.1038/nature07341

Cited by 846 publications

(866 citation statements)

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“…This research has demonstrated that polyploidy can influence many important individual‐ and population‐level traits, ranging from likely positive effects such as increased enzymatic activity (Levin 1983), higher levels of gene expression (De Godoy et al. 2008; Neiman et al. 2009), and greater adaptive potential (Otto and Whitton 2000; Balao et al.…”

Section: Introductionmentioning

confidence: 99%

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Effects of polyploidy and reproductive mode on life history trait expression

Larkin

Tucci

Neiman

2016

Ecology and Evolution

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Ploidy elevation is increasingly recognized as a common and important source of genomic variation. Even so, the consequences and biological significance of polyploidy remain unclear, especially in animals. Here, our goal was to identify potential life history costs and benefits of polyploidy by conducting a large multiyear common garden experiment in Potamopyrgus antipodarum, a New Zealand freshwater snail that is a model system for the study of ploidy variation, sexual reproduction, host–parasite coevolution, and invasion ecology. Sexual diploid and asexual triploid and tetraploid P. antipodarum frequently coexist, allowing for powerful direct comparisons across ploidy levels and reproductive modes. Asexual reproduction and polyploidy are very often associated in animals, allowing us to also use these comparisons to address the maintenance of sex, itself one of the most important unresolved questions in evolutionary biology. Our study revealed that sexual diploid P. antipodarum grow and mature substantially more slowly than their asexual polyploid counterparts. We detected a strong negative correlation between the rate of growth and age at reproductive maturity, suggesting that the relatively early maturation of asexual polyploid P. antipodarum is driven by relatively rapid growth. The absence of evidence for life history differences between triploid and tetraploid asexuals indicates that ploidy elevation is unlikely to underlie the differences in trait values that we detected between sexual and asexual snails. Finally, we found that sexual P. antipodarum did not experience discernable phenotypic variance‐related benefits of sex and were more likely to die before achieving reproductive maturity than the asexuals. Taken together, these results suggest that under benign conditions, polyploidy does not impose obvious life history costs in P. antipodarum and that sexual P. antipodarum persist despite substantial life history disadvantages relative to their asexual counterparts.

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Section: Introductionmentioning

confidence: 99%

“…For example, if polyploids have higher per‐organism gene expression ( e.g ., De Godoy et al. 2008; Neiman et al. 2009), the positive correlation between organismal RNA content and growth rate (Hessen et al.…”

Section: Introductionmentioning

confidence: 99%

Effects of polyploidy and reproductive mode on life history trait expression

Larkin

Tucci

Neiman

2016

Ecology and Evolution

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“…Bioinformatics / Data management / Laboratory information management system / Mascot / MS Proteomics labs nowadays often acquire hundreds of thousands to millions of MS/MS spectra per proteome analysis to make large-scale (comprehensive) proteome maps [1]. They rely on contemporary mass spectrometers with rapid duty cycles that increase the amount of produced data by a full order of magnitude compared to older instruments [2].…”

Section: Introductionmentioning

confidence: 99%

ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics

et al. 2010

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MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. Highthroughput studies require automation of these various steps, and management of the data in association with the results obtained. We here present ms_lims (http://genesis.UGent.be/ ms_lims), a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses. Keywords:Bioinformatics / Data management / Laboratory information management system / Mascot / MS Proteomics labs nowadays often acquire hundreds of thousands to millions of MS/MS spectra per proteome analysis to make large-scale (comprehensive) proteome maps [1]. They rely on contemporary mass spectrometers with rapid duty cycles that increase the amount of produced data by a full order of magnitude compared to older instruments [2]. Automating the processing of these data, and managing their provenance has correspondingly become an important postanalysis task. The automation of these tasks requires the implementation of a start-to-end workflow around a central database management system that is designed for proteomics experiments, with some of the most prominent commercial and academic systems recently reviewed in [3]. Typical actions include collecting and warehousing MS/MS peak lists (often acquired on multiple, different instruments), assigning the accumulated MS/MS data to peptide identifications, quantifying peptides and proteins from MS or MS/MS data, and organizing both data and analysis results in a navigable project structure. In most high-throughput environments, these diverse actions are typically undertaken by different individuals, which further necessitates a role-based implementation of the software interfaces [4].To tackle and manage these problems associated with MSdriven proteomics, we developed ms_lims, an open source and instrument vendor-independent system for proteomics data management. In contrast to existing web-based tools such as MASPECTRAS [4] or CPAS [5], ms_lims embraces a client-server architecture, which allows for more dynamic interaction. Additionally, ms_lims also differs from libraries Abbreviations: LIMS, laboratory information management system; MGF, Mascot generic file; SQL, Structured Query Language Ã These authors contributed equally to this work.

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“…Les articles les plus marquants se sont intéressés à l'étude des voies de signalisation activées par l'EGF (epidermal growth factor) dans les cellules mammifères [26,27] ou par les phéromones chez la levure [28,29].…”

Section: Applicationsunclassified

La protéomique quantitative par la méthode SILAC

Emadali

Gallagher-Gambarelli

2009

Med Sci (Paris)

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La protéomique quantitative GénéralitésLe domaine de la protéomique -définie comme l'étude de l'ensemble des protéines d'un échantillon biologique donné -s'est développé de façon spectaculaire au cours des dernières années [1,2]. Les progrès majeurs réalisés dans le domaine de l'instrumentation pour la protéomi-que (spectrométrie de masse, chromatographie liquide nano-débit), associés à la masse d'informations sans cesse croissante disponible dans les banques de données et à la conception de nouveaux outils logiciels, ont conduit à la mise en place de stratégies qui permettent d'analyser le protéome des échantillons biologiques de manière efficace et fiable. Ainsi, des inventaires de protéines de plus en plus complets ont pu être établis dans le cadre de travaux menés chez l'homme et chez des organismes modèles. Indéniablement, ces inventaires réalisés à partir d'échantillons plus ou moins complexes et ciblés (tissus, cellules, compartiments subcellulaires, complexes protéiques, etc.) ont participé à une meilleure connaissance des acteurs moléculaires impliqués dans les grands « mécanismes du vivant ». Le principe général d'une analyse protéomique est pré-senté dans la Figure 1 et > Les approches de protéomique quantitative basées sur la spectrométrie de masse sont parfaitement adaptées à la détection de changements au niveau protéique entre échantillons biologiques. Parmi ces techniques, la méthode SILAC (stable isotope labelling by amino acids in cell culture) a démontré un réel potentiel. Cette méthode s'avère en effet être précise et relativement simple à mettre en oeuvre pour quantifier les protéines extraites de cellules en culture. Le principe est le suivant : les cellules sont cultivées dans un milieu contenant soit des acides aminés naturels (synthèse de protéines « légères »), soit leurs équivalents isotopiquement marqués (synthèse de protéines « lourdes »). Les populations cellulaires à comparer sont mélangées et traitées comme un seul échantillon, ce qui permet de préparer les protéines d'intérêt sans risquer d'introduire des erreurs de quantification. Au cours de l'analyse par spectrométrie de masse, l'abondance relative entre les échantillons biologiques peut être calculée pour chaque protéine en comparant l'intensité des peptides légers et lourds. Comme le montrent ses applications à diverses problématiques biologiques et cliniques, la méthode SILAC est particulièrement prometteuse pour l'élucidation des mécanismes moléculaires impliqués dans les grandes fonctions cellulaires, ainsi que pour l'identification de biomarqueurs de maladies. La limitation de la méthode SILAC à la quantification de protéines issues de cellules en culture vient d'être levée suite à la description d'une souris SILAC dont toutes les protéines sont marquées isotopiquement. Ces travaux laissent présager une extension de cette stratégie analytique à l'étude différentielle de tissus et de fluides biologiques d'animaux modèles. < Article disponible sur le site

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Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

Cited by 846 publications

References 28 publications

Effects of polyploidy and reproductive mode on life history trait expression

Effects of polyploidy and reproductive mode on life history trait expression

ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics

La protéomique quantitative par la méthode SILAC

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