Dataset Information

IPRG 2012: A Study on Detecting Modified Peptides in a Complex Mixture

ABSTRACT: This is the data and results associated with the 2012 study organized by the proteome informatics research group of the Association of Biomolecular Resource Facilities, which investigated participants' ability to identify a range of post-translationally modified peptides spiked into a yeast lysate background. Results and analysis of this study were published in Molecular and Cellular Proteomics: Chalkley RJ, Bandeira N, Chambers MC, Clauser K, Cottrell J, Deutsch EW, Kapp EA, Lam HH, McDonald WH, Neubert TA, Sun RX Mol Cell Proteomics 2013 [Epub Oct 31]

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Robert Chalkley

PROVIDER: MSV000078492 | MassIVE | Tue Nov 19 16:45:00 GMT 2013

REPOSITORIES: MassIVE

ACCESS DATA

Publications

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

Chalkley Robert J RJ Bandeira Nuno N Chambers Matthew C MC Clauser Karl R KR Cottrell John S JS Deutsch Eric W EW Kapp Eugene A EA Lam Henry H N HH McDonald W Hayes WH Neubert Thomas A TA Sun Rui-Xiang RX

Molecular & cellular proteomics : MCP 20131031 1

The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community's ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring modifications combined with a yeast whole cell lysate as background was distributed to a large group of research ...[more]

PMID: 24187338

Similar Datasets

Project description:Tissue samples in biobanks preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature (OCT)-embedded and subsequently freezing are highly valuable in experimental studies where the results can be related to clinical parameters. Today, mass spectrometry (MS)-based proteomics is the method of choice for unbiased and relative comparison of the abundances of thousands of proteins present in biological samples. MS analysis of FFPE- and OCT-preserved tissue has been limited, but it is now approachable using newly developed protocols. However, it has not been clarified how the results from different preservation methods agrees and differ. In this study, we use a unique sample set of urinary bladder cancer tissues of two different tumor stages (Ta/T1 – non-muscle invasive and T2/T3 muscle invasive); upon sampling the tumors were divided and preserved by the two methods. Thereafter a protocol for parallel processing of the samples were applied after which the samples were analyzed with label free quantitative MS analysis. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Principal component analysis showed that the largest differences between samples are based on the preservation method, but this analysis could also classify the tumors into different stages in each preservation. The overlap of quantifiable proteins between the preservation methods were 84% when all proteins and full data set were taken into consideration, but only 41% on average when proteins from a specific tumor were analyzed. Proteins involved in mitochondrial function were overrepresented among proteins present in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Moreover, univariate analysis showed that HMGCS2 protein is uniquely quantified in Ta/T1 tumors in both FFPE and OCT data, and that LGALS1, ANXA5 and plastin proteins are upregulated in T2/T3 tumors compared to Ta/T1 tumors in both FFPE and OCT data, confirming the consistency between the data sets and suggesting these proteins as biomarkers. Finally, LGALS1 data were verified by immunohistochemistry staining of an independent data set.

Project description:One of the most important issues in the study of aging is to discover compounds with longevity-promoting activity and to unravel their underlying mechanisms. Queen honey bees are continuously fed royal jelly (RJ), and they live more than 10 times longer than hive workers, derived from the same diploid genome, which are fed it only for a short period of time during their larval stages. Therefore, RJ is likely to contain longevity-promoting agents for queens. RJ has been reported to possess diverse pharmacological properties. Furthermore, protease-treated RJ (pRJ) has additional beneficial activities. How RJ and pRJ exert these effects and which components in them play a critical role is largely unknown. The evolutionally conserved mechanisms that control lifespan have been indicated. The nematode Caenorhabditis elegans has been widely used for study of aging and longevity, due to its relatively short lifespan and well-established genetic pathways. The purpose of the present study was to elucidate whether RJ and its related substances contain the life span-extending activity in C. elegans and to obtain some insight into the active agents and their mechanisms. We found that both RJ and pRJ extended the lifespan of C. elegans. The life span-extending activity of pRJ was enriched by ODS column chromatography (pRJ-Fraction 5). pRJ-Fr. 5 extended the life span partly by acting through the FOXO transcription factor DAF-16, the activation of which is known to promote longevity in C. elegans by reducing insulin/IGF-1 signaling (IIS). pRJ-Fr. 5 induced changes in the expression of 3 genes encoding insulin-like peptides. Moreover, pRJ-Fr. 5 and reduced IIS shared some common features in terms of their effect on gene expression, such as up-regulation of dod-3 and down-regulation of dod-19, dao-4 and fkb-4. The dod-19 is a previously identified life span determinant in C. elegans, and the fkb-4 encodes a homologue of the mammalian FK506-binding protein. 10-Hydroxy-2-decenoic acid (10-HDA), which was present in high concentration in pRJ-Fr. 5, increased the lifespan independently of DAF-16 activity.These results demonstrate that RJ and its related substances extended the life span in C. elegans, suggesting that RJ may contain longevity-promoting factors common to diverse species across phyla. pRJ-Fr. 5 had higher life span-extending activity than either RJ or pRJ and extended the life span in part through the IIS-DAF-16 pathway. We provide the first evidence that 10-HDA, a defined natural product in RJ, extended organismal lifespan. It is noteworthy that 10-HDA performed its lifespan-extending function through a mechanism totally different from the IIS-DAF-16 pathway. Further search and characterization of the lifespan-extending agents in RJ and pRJ may broaden our understanding of the gene network of longevity regulation in diverse species and provide the possibility for nutraceutical interventions in the aging process.

Dataset Information

IPRG 2012: A Study on Detecting Modified Peptides in a Complex Mixture

Publications

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure