RT Journal Article
SR Electronic
T1 piNET: a versatile web platform for downstream analysis and visualization of proteomics data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 607432
DO 10.1101/607432
A1 Behrouz Shamsaei
A1 Szymon Chojnacki
A1 Marcin Pilarczyk
A1 Mehdi Najafabadi
A1 Chuming Chen
A1 Karen Ross
A1 Andrea Matlock
A1 Jeremy Muhlich
A1 Somchai Chutipongtanate
A1 Dusica Vidovic
A1 Vagisha Sharma
A1 Juozas Vasiliauskas
A1 Jake Jaffe
A1 Michael MacCoss
A1 Cathy Wu
A1 Ajay Pillai
A1 Avi Ma’ayan
A1 Stephan Schurer
A1 Mario Medvedovic
A1 Jarek Meller
YR 2019
UL http://biorxiv.org/content/early/2019/04/12/607432.abstract
AB Large 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, require 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.