The University of Southampton
University of Southampton Institutional Repository

OPBI: an open pipeline for biomarker identification

OPBI: an open pipeline for biomarker identification
OPBI: an open pipeline for biomarker identification

Biomarker discovery is one particular pipeline utilized in shotgun proteomics, which is made up of series of phases starting from a set of mass spectrum files and ending with some significantly expressed proteins that are related to a particular disease condition. Different techniques and tools have been introduced to perform protein identification and biomarker identification, and they still consume days/hours to carry out the processes. Further, they ignore MS1 information and consider only the information included in MS2 spectra. In this paper, we present an open-source, R-based, accurate biomarker identification pipeline, which provides solutions to time consumption problem in current biomarker discovery pipelines and utilizes the information of MS1 spectra. The developed pipeline was validated using three raw datasets of PRIDE database. We observed around 2-4 times speed-up and FDR ranges from 0.0003 to 0.0009. The biomarker identification system is accurate and operates in a considerable speed than commonly used, open-source MaxQuant tool.

biomarkers, Open-source, shotgun-proteomics
1510-1514
IEEE Computer Society
Vidanagamachchi, Sugandima
f848309d-09d2-41cf-97bb-efa083558da8
Niranjan, Mahesan
5cbaeea8-7288-4b55-a89c-c43d212ddd4f
Vidanagamachchi, Sugandima
f848309d-09d2-41cf-97bb-efa083558da8
Niranjan, Mahesan
5cbaeea8-7288-4b55-a89c-c43d212ddd4f

Vidanagamachchi, Sugandima and Niranjan, Mahesan (2018) OPBI: an open pipeline for biomarker identification. In 2017 IEEE International Conference on Industrial Engineering and Engineering Management, IEEM 2017. vol. 2017-December, IEEE Computer Society. pp. 1510-1514 . (doi:10.1109/IEEM.2017.8290145).

Record type: Conference or Workshop Item (Paper)

Abstract

Biomarker discovery is one particular pipeline utilized in shotgun proteomics, which is made up of series of phases starting from a set of mass spectrum files and ending with some significantly expressed proteins that are related to a particular disease condition. Different techniques and tools have been introduced to perform protein identification and biomarker identification, and they still consume days/hours to carry out the processes. Further, they ignore MS1 information and consider only the information included in MS2 spectra. In this paper, we present an open-source, R-based, accurate biomarker identification pipeline, which provides solutions to time consumption problem in current biomarker discovery pipelines and utilizes the information of MS1 spectra. The developed pipeline was validated using three raw datasets of PRIDE database. We observed around 2-4 times speed-up and FDR ranges from 0.0003 to 0.0009. The biomarker identification system is accurate and operates in a considerable speed than commonly used, open-source MaxQuant tool.

Full text not available from this repository.

More information

e-pub ahead of print date: 9 February 2018
Published date: 12 February 2018
Venue - Dates: 2017 IEEE International Conference on Industrial Engineering and Engineering Management, IEEM 2017, Singapore, Singapore, 2017-12-10 - 2017-12-13
Keywords: biomarkers, Open-source, shotgun-proteomics

Identifiers

Local EPrints ID: 420129
URI: https://eprints.soton.ac.uk/id/eprint/420129
PURE UUID: d41f263c-ef1e-4f86-8c65-21b08810efad

Catalogue record

Date deposited: 27 Apr 2018 16:30
Last modified: 13 Mar 2019 18:34

Export record

Altmetrics

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of https://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×