ColPTMScape: An open access knowledge base for tissue-specific collagen PTM maps

Ashutosh Joshi; Ayush Nigam; Lalit Narayan Mudgal; Bhaskar Mondal; Trayambak Basak

doi:10.1016/j.mbplus.2024.100144

ColPTMScape: An open access knowledge base for tissue-specific collagen PTM maps

Matrix Biol Plus. 2024 Feb 29:22:100144. doi: 10.1016/j.mbplus.2024.100144. eCollection 2024 Jun.

Authors

Ashutosh Joshi¹, Ayush Nigam¹, Lalit Narayan Mudgal¹, Bhaskar Mondal², Trayambak Basak¹

Affiliations

¹ School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India.
² School of Chemical Sciences, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India.

Abstract

Collagen is a key component of the extracellular matrix (ECM). In the remodeling of ECM, a remarkable variation in collagen post-translational modifications (PTMs) occurs. This makes collagen a potential target for understanding extracellular matrix remodeling during pathological conditions. Over the years, scientists have gathered a huge amount of data about collagen PTM during extracellular matrix remodeling. To make such information easily accessible in a consolidated space, we have developed ColPTMScape (https://colptmscape.iitmandi.ac.in/), a dedicated knowledge base for collagen PTMs. The identified site-specific PTMs, quantitated PTM sites, and PTM maps of collagen chains are deliverables to the scientific community, especially to matrix biologists. Through this knowledge base, users can easily gain information related to the difference in the collagen PTMs across different tissues in different organisms.

Keywords: Collagen; Collagen PTMs; Extracellular matrix; Knowledge base; PTM identification; PTM quantitation.