Proteomics

Dataset Information

0

Method to identify novel proteoform peptides from salivary supernatant.

ABSTRACT: We describe the use Galaxy framework to facilitate complete proteogenomic analysis for a representative salivary dataset. We demonstrate how Galaxy’s many features make it a unique and ideal solution for proteogenomic analysis. We highlight Galaxy’s flexibility by creating a modular workflow incorporating both established and customized software and processing steps that improve depth and quality of proteogenomic results. We demonstrate Galaxy’s accessibility, via the easy sharing of complete, and even complex (approximately 140 steps), proteogenomic workflows, which can be used and customized by others via a public instance of the framework (usegalaxyp.org). Our results provide a blueprint for the establishment of the Galaxy framework as an ideal solution for the emerging field of proteogenomics.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Saliva

DISEASE(S): Disease Free

SUBMITTER: Pratik Jagtap  

LAB HEAD: Timothy Griffin

PROVIDER: PXD000991 | Pride | 2015-01-05

REPOSITORIES: Pride

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Publications

Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.

Jagtap Pratik D PD   Johnson James E JE   Onsongo Getiria G   Sadler Fredrik W FW   Murray Kevin K   Wang Yuanbo Y   Shenykman Gloria M GM   Bandhakavi Sricharan S   Smith Lloyd M LM   Griffin Timothy J TJ  

Journal of proteome research 20141023 12

Proteogenomics combines large-scale genomic and transcriptomic data with mass-spectrometry-based proteomic data to discover novel protein sequence variants and improve genome annotation. In contrast with conventional proteomic applications, proteogenomic analysis requires a number of additional data processing steps. Ideally, these required steps would be integrated and automated via a single software platform offering accessibility for wet-bench researchers as well as flexibility for user-speci  ...[more]

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