phpMs: A PHP-Based Mass Spectrometry Utilities Library

Collins, Andrew ORCID: 0000-0003-0507-6912 and Jones, Andrew R ORCID: 0000-0001-6118-9327 (2018) phpMs: A PHP-Based Mass Spectrometry Utilities Library. JOURNAL OF PROTEOME RESEARCH, 17 (3). pp. 1309-1313.

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Official URL: http://dx.doi.org/10.1021/acs.jproteome.7b00783

Abstract

The recent establishment of cloud computing, high-throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimized desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualized in a high-quality cross-platform interface via a web browser. There are number of emerging platforms for cloud-based mass spectrometry data analysis; however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider. To remedy this, we provide an open-source mass spectrometry library for one of the most commonly used web development languages, PHP. Our new library, phpMs, provides objects for storing and manipulating spectra and identification data as well as utilities for file reading, file writing, calculations, peptide fragmentation, and protein digestion as well as a software interface for controlling search engines. We provide a working demonstration of some of the capabilities at http://pgb.liv.ac.uk/phpMs .

Item Type:	Article
Uncontrolled Keywords:	phpMs, PHP, proteomics, library, bioinformatics, software, mass spectrometry
Depositing User:	Symplectic Admin
Date Deposited:	02 Mar 2020 15:51
Last Modified:	19 Jan 2023 00:00
DOI:	10.1021/acs.jproteome.7b00783
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3076756