piNET: a versatile web platform for downstream analysis and visualization of proteomics data [article]

Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Najafabadi, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Dusica Vidovic, Vagisha Sharma, Juozas Vasiliauskas (+8 others)
2019 bioRxiv   pre-print
ABSTRACTLarge proteomics data, including those generated by mass spectrometry, are being generated to characterize biological systems at the protein level. Computational methods and tools to identify and quantify peptides, proteins and post-translational modifications (PTMs) that are captured in modern mass spectrometers have matured over the years. On the other hand, tools for downstream analysis, interpretation and visualization of proteomics data sets, in particular those involving PTMs,
more » ... ire further improvement and integration to accelerate scientific discovery and maximize the impact of proteomics studies by connecting them better with biological knowledge across not only proteomics, but also other Omics domains. With the goal of addressing these challenges, the piNET server has been developed as a versatile web platform to facilitate mapping, annotation, analysis and visualization of peptide, PTM, and protein level quantitative data generated by either targeted, shotgun or other proteomics approaches. Building on our experience with large scale analysis of gene and protein expression profiles as part of the Library of Integrated Network Cellular Signatures (LINCS) project, piNET has been designed as a fast, versatile and easy to use web-based tool with three modules that provide mapping from peptides (with PTMs) to proteins, from PTM sites to modifying enzymes that target those sites, and finally from proteins (with PTMs) to pathways, and for further mechanistic insights to LINCS signatures of chemical and genetic perturbations. piNET is freely available at http://www.pinet-server.org.
doi:10.1101/607432 fatcat:d5yluyxpyfbpzoqksczhun3zwe