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

Q2 Decision Sciences

Source Code for Biology and Medicine Pub Date : 2018-11-12 eCollection Date: 2018-01-01 DOI:10.1186/s13029-018-0070-0

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

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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.

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ProSave:用于将定量数据恢复到被操纵的蛋白质列表子集的应用程序。

背景:在蛋白质组学研究中，液相色谱串联质谱数据(LC-MS/MS)是通过光谱计数或一些离子丰度测量来量化的。蛋白质含量的下游比较分析(如维恩图和网络分析)通常不包括这种定量数据，关键信息经常丢失。为了避免在比较蛋白质组学分析中丢失光谱计数数据，实现一个可以快速检索这些信息的工具是至关重要的。结果:我们开发了ProSave，这是一个免费且用户友好的基于java的程序，可以从大型蛋白质组学数据集中的蛋白质列表中检索光谱计数数据。ProSave允许管理LC-MS/MS数据集，并快速检索所需蛋白质列表的光谱计数信息。结论:ProSave是开源的，可以在https://github.com/MahajanLab/ProSave免费获得。用户手册、实现说明、方法描述和示例都可以在网站上找到。

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Source Code for Biology and Medicine Decision Sciences-Information Systems and Management

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期刊介绍： Source Code for Biology and Medicine is a peer-reviewed open access, online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. The journal"s aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.