ISPIDER Central: an integrated database web-server for proteomics

Siepen, Jennifer A.; Belhajjame, Khalid; Selley, Julian N.; Embury, Suzanne M.; Paton, Norman W.; Goble, Carole; Oliver, Stephen G.; Stevens, Robert; Zamboulis, Lucas; Martin, Nigel; Poulovassillis, Alexandra; Jones, Philip; Côté, Richard J.; Hermjakob, Henning; Pentony, Melissa M; Jones, David T.; Orengo, Christine A.; Hubbard, Simon J.

doi:10.1093/nar/gkn196

Cited by 20 publications

(13 citation statements)

References 30 publications

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“…For this purpose, several repositories have become available to search for previously carried‐out proteomic experiments, and PRIDE 20, PepSeeker 21, PeptideAtlas 22, the NIST data set (available at http://peptide.nist.gov/) and GPM 23 have emerged as the main databases in this category. The meta‐search engine ISPIDER 24 can search for similar proteomic experiments and peptide identifications in all these databases simultaneously, thus enabling potentially interesting comparisons to previously published studies.…”

Section: First Stepsmentioning

confidence: 99%

From proteome lists to biological impact– tools and strategies for the analysis of large MS data sets

et al. 2010

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MS has become a method-of-choice for proteome analysis, generating large data sets, which reflect proteome-scale protein-protein interaction and PTM networks. However, while a rapid growth in large-scale proteomics data can be observed, the sound biological interpretation of these results clearly lags behind. Therefore, combined efforts of bioinformaticians and biologists have been made to develop strategies and applications to help experimentalists perform this crucial task. This review presents an overview of currently available analytical strategies and tools to extract biologically relevant information from large protein lists. Moreover, we also present current research publications making use of these tools as examples of how the presented strategies may be incorporated into proteomic workflows. Emphasis is placed on the analysis of Gene Ontology terms, interaction networks, biological pathways and PTMs. In addition, topics including domain analysis and text mining are reviewed in the context of computational analysis of proteomic results. We expect that these types of analyses will significantly contribute to a deeper understanding of the role of individual proteins, protein networks and pathways in complex systems.

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Section: First Stepsmentioning

confidence: 99%

From proteome lists to biological impact– tools and strategies for the analysis of large MS data sets

et al. 2010

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“…For example, many algorithms and software tools have been developed to expedite assay development by aiding in the selection of proteotypic peptides (31), peptide transitions, and instrument parameters (reviewed in Cham Mead et al (32)). Additionally, through community effort, several publicly available databases of tandem MS spectra (33)(34)(35)(36)(37)(38)(39) and validated SRM assays (40,41) are available to provide empirical guides to transition selection and assay development. Several groups have also presented elegant solutions to maximize instrument duty cycle and improve assay specificity.…”

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confidence: 99%

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

Peterson

Russell

Bailey

et al. 2012

Molecular & Cellular Proteomics

1,109

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Selected reaction monitoring on a triple quadrupole mass spectrometer is currently experiencing a renaissance within the proteomics community for its, as yet, unparalleled ability to characterize and quantify a set of proteins reproducibly, completely, and with high sensitivity. Given the immense benefit that high resolution and accurate mass instruments have brought to the discovery proteomics field, we wondered if highly accurate mass measurement capabilities could be leveraged to provide benefits in the targeted proteomics domain as well. Here, we propose a new targeted proteomics paradigm centered on the use of next generation, quadrupole-equipped high resolution and accurate mass instruments: parallel reaction monitoring (PRM). In PRM, the third quadrupole of a triple quadrupole is substituted with a high resolution and accurate mass mass analyzer to permit the parallel detection of all target product ions in one, concerted high resolution mass analysis. We detail the analytical performance of the PRM method, using a quadrupoleequipped bench-top Orbitrap MS, and draw a performance comparison to selected reaction monitoring in terms of run-to-run reproducibility, dynamic range, and measurement accuracy. In addition to requiring minimal upfront method development and facilitating automated data analysis, PRM yielded quantitative data over a wider dynamic range than selected reaction monitoring in the presence of a yeast background matrix because of PRM's high selectivity in the mass-to-charge domain. With achievable linearity over the quantifiable dynamic range found to be statistically equal between the two methods, our investigation suggests that PRM will be a promising new addition to the quantitative proteomics toolbox. Molecular & Cellular Proteomics 11: 10.1074/ mcp.O112.020131, 1475-1488, 2012.The most widespread protein sequencing technique is the shotgun method. Proteins are digested into peptides, chromatographically separated, and measured by mass spectrometers (1-10). Many types of mass spectrometers are used-quadrupole ion traps, quadrupole ion trap hybrids such as the QLT (quadrupole linear ion trap)-Orbitrap or QLT-FT-ICR, and quadrupole time-of-flight (Q-TOF) hybrids-but, the experiments, from the MS measurement onward, are basically identical: the masses of eluting cationic peptide precursors are measured in a MS scan, and the most abundant precursors are selected in series for successive tandem MS events (MS/MS). This process, called data-dependent acquisition, continues for the duration of a chromatographic separation, and constant MS operation in this manner can generate hundreds of thousands of spectra in days. These spectra are then mapped to peptide or protein sequence databases using highly-evolved database search algorithms (11-13). Successful results can be obtained within just a few days and are nothing short of spectacular: tens of thousands of unique peptide spectral matches mapping to several thousand unique protein isoforms have become the norm. Although this approach certainly ...

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“…Being aware of the potential errors in localization mentioned above, we used comparative genomics to validate our predictions. We aligned the candidate scaffolds to the Human genome and identified the surrounding homologous region on the pig genome from conserved syntenies predicted by the Narcisse comparative genome browser [29]. We classified the validation results into 5 categories (Table 2): …”

Section: Resultsmentioning

confidence: 99%

High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly

et al. 2012

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BackgroundThe release of the porcine genome sequence offers great perspectives for Pig genetics and genomics, and more generally will contribute to the understanding of mammalian genome biology and evolution. The process of producing a complete genome sequence of high quality, while facilitated by high-throughput sequencing technologies, remains a difficult task. The porcine genome was sequenced using a combination of a hierarchical shotgun strategy and data generated with whole genome shotgun. In addition to the BAC contig map used for the clone-by-clone approach, genomic mapping resources for the pig include two radiation hybrid (RH) panels at two different resolutions. These two panels have been used extensively for the physical mapping of pig genes and markers prior to the availability of the pig genome sequence.ResultsIn order to contribute to the assembly of the pig genome, we genotyped the two radiation hybrid (RH) panels with a SNP array (the Illumina porcineSNP60 array) and produced high density physical RH maps for each pig autosome. We first present the methods developed to obtain high density RH maps with 38,379 SNPs from the SNP array genotyping. We then show how they were useful to identify problems in a draft of the pig genome assembly, and how the RH maps enabled the problems to be corrected in the porcine genome sequence. Finally, we used the RH maps to predict the position of 2,703 SNPs and 1,328 scaffolds currently unplaced on the porcine genome assembly.ConclusionsA complete process, from genotyping of a high density SNP array on RH panels, to the construction of genome-wide high density RH maps, and finally their exploitation for validating and improving a genome assembly is presented here. The study includes the cross-validation of RH based findings with independent information from genetic data and comparative mapping with the Human genome. Several additional resources are also provided, in particular the predicted genomic location of currently unplaced SNPs and associated scaffolds summing up to a total of 72 megabases, that can be useful for the exploitation of the pig genome assembly.

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ISPIDER Central: an integrated database web-server for proteomics

Cited by 20 publications

References 30 publications

From proteome lists to biological impact– tools and strategies for the analysis of large MS data sets

From proteome lists to biological impact– tools and strategies for the analysis of large MS data sets

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly

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