ProSave: an application for restoring quantitative data to manipulated subsets of protein lists

Daniel A Machlab; Gabriel Velez; Alexander G Bassuk; Vinit B Mahajan

doi:10.1186/s13029-018-0070-0

Back

ProSave: an application for restoring quantitative data to manipulated subsets of protein lists

Journal article

Open access

Peer reviewed

ProSave: an application for restoring quantitative data to manipulated subsets of protein lists

Daniel A Machlab, Gabriel Velez, Alexander G Bassuk and Vinit B Mahajan

Source code for biology and medicine, Vol.13(1), pp.3-3

11/12/2018

DOI: 10.1186/s13029-018-0070-0

PMCID: PMC6233572

PMID: 30459825

Files and links (1)

url

https://doi.org/10.1186/s13029-018-0070-0View

Published (Version of record) Open Access

Abstract

Background: In proteomics studies, liquid chromatography tandem mass spectrometry data (LC-MS/MS) is quantified by spectral counts or by some measure of ion abundance. Downstream comparative analysis of protein content (e.g. Venn diagrams and network analysis) typically does not include this quantitative data and critical information is often lost. To avoid loss of spectral count data in comparative proteomic analyses, it is critical to implement a tool that can rapidly retrieve this information. Results: We developed ProSave, a free and user-friendly Java-based program that retrieves spectral count data from a curated list of proteins in a large proteomics dataset. ProSave allows for the management of LC-MS/MS datasets and rapidly retrieves spectral count information for a desired list of proteins. Conclusions: ProSave is open source and freely available at https://github.com/MahajanLab/ProSave. The user manual, implementation notes, and description of methodology and examples are available on the site.

Software

Proteomics

Java

ProSave

Precision medicine

Details

Title: Subtitle: ProSave: an application for restoring quantitative data to manipulated subsets of protein lists
Creators: Daniel A Machlab - Palo Alto, CA USA
Gabriel Velez - Palo Alto, CA USA
Alexander G Bassuk - Iowa City, IA USA
Vinit B Mahajan - Palo Alto, CA USA
Resource Type: Journal article
Publication Details: Source code for biology and medicine, Vol.13(1), pp.3-3
DOI: 10.1186/s13029-018-0070-0
PMID: 30459825
PMCID: PMC6233572
NLM abbreviation: Source Code Biol Med
ISSN: 1751-0473
eISSN: 1751-0473
Publisher: BioMed Central; London
Grant note: ; 2013103 / ; R01EY026682, R01EY024665, R01EY025225, R01EY024698, R21AG050437, and P30EY026877; F30EYE027986 and T32GM007337 / ;
Language: English
Date published: 11/12/2018
Academic Unit: Neurology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Neurology (Pediatrics)
Record Identifier: 9984070822902771

Metrics

21 Record Views