Data Independent Acquisition analysis in ProHits 4.0

作者：Liu Guomin; Knight James D R; Zhang Jian Ping; Tsou Chih Chiang; Wang Jian; Lambert Jean Philippe; Larsen Brett; Tyers Mike; Raught Brian; Bandeira Nuno; Nesvizhskii Alexey I; Choi Hyungwon; Gingras Anne Claude^*

来源：Journal of Proteomics, 2016, 149: 64-68.

DOI：10.1016/j.jprot.2016.04.042

• Laboratory Information Management System
• Mass spectrometry
• Data Independent Acquisition
• Protein-protein interactions
• Affinity purification coupled to mass spectrometry
• Proteomics

Affinity purification coupled with mass spectrometry (AP-MS) is a powerful technique for the identification and quantification of physical interactions. AP-MS requires careful experimental design, appropriate control selection and quantitative workflows to successfully identify bona fide interactors amongst a large background of contaminants. We previously introduced ProHits, a Laboratory Information Management System for interaction proteomics, which tracks all samples in a mass spectrometry facility, initiates database searches and provides visualization tools for spectral counting-based AP-MS approaches. More recently, we implemented Significance Analysis of INTeractome (SAINT) within ProHits to provide scoring of interactions based on spectral counts. Here, we provide an update to ProHits to support Data Independent Acquisition (DIA) with identification software (DIA-Umpire and MSPLIT-DIA), quantification tools (through DIA-Umpire, or externally via targeted extraction), and assessment of quantitative enrichment (through mapDlA) and scoring of interactions (through SAINT intensity). With additional improvements, notably support of the iProphet pipeline, facilitated deposition into ProteomeXchange repositories and enhanced export and viewing functions, ProHits 4.0 offers a comprehensive suite of tools to facilitate affinity proteomics studies.
Significance: It remains challenging to score, annotate and analyze proteomics data in a transparent manner. ProHits was previously introduced as a LIMS to enable storing, tracking and analysis of standard AP-MS data. In this revised version, we expand ProHits to include integration with a number of identification and quantification tools based on Data-Independent Acquisition (DIA). ProHits 4.0 also facilitates data deposition into public repositories, and the transfer of data to new visualization tools.

• 出版日期2016-10-21