Research Article

PeptideDepot: Flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information

  1. Kebing Yu1,
  2. Arthur R. Salomon1,2,3,*

Article first published online: 15 OCT 2009

DOI: 10.1002/pmic.200900119

Issue

PROTEOMICS

PROTEOMICS

Volume 9, Issue 23, pages 5350–5358, No. 23 December 2009

Additional Information

How to Cite

Yu, K. and Salomon, A. R. (2009), PeptideDepot: Flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information. PROTEOMICS, 9: 5350–5358. doi: 10.1002/pmic.200900119

Author Information

  1. 1

    Department of Chemistry, Brown University, RI, USA

  2. 2

    Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, RI, USA

  3. 3

    Center for Genomics and Proteomics, Brown University, RI, USA

*Brown University, 70 Ship Street, Providence, RI 02903, USA Fax: +1-401-863-6087

Publication History

  1. Issue published online: 16 DEC 2009
  2. Article first published online: 15 OCT 2009
  3. Manuscript Accepted: 1 SEP 2009
  4. Manuscript Revised: 29 JUL 2009
  5. Manuscript Received: 22 FEB 2009

Funded by

  • National Institutes of Health. Grant Number: 2P20RR015578

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Keywords:

  • Bioinformatic;
  • Peptide repository;
  • Quantitative proteomics;
  • Relational database;
  • Visualization

Abstract

Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker-driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end-users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post-acquisition analysis of proteomic data.

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