Dr. Khalid Mehmood Ul Hasan

The cycle of life on Earth is fueled through one single most important entity, protein, which has major implications in almost every aspect of human life. Over the last few decades general public of Pakistan has been exposed to slow poisoning caused by contaminated water. This water contains hazardous amount of heavy metals which get absorbed by the bacteria through the process of Biosorption leading to the vast phenomenon of Microbial Fixation. Due to rapid industrialization, the fixation process is deteriorating at an alarming rate, and hence, as a result of seepage through drains, the underground water table is at risk. Identification and quantitation of proteins responsible for microbial fixation, the only natural process to remove hazardous heavy metals from the water, can help us unlocking a plethora of ways to combat the issue of heavy metal contamination in Pakistan. Determining the protein content of these bacteria can lead. Our tool is free, open source and open architecture web service that provides an intuitive search environment for identifying and quantifying proteins. In this work, we extend our tool for analyzing top-down proteomics data by incorporating a much-needed top down protein quantitation tool. Currently its salient features include: (i) intensity weighted sliding window protocol for intact protein mass tuning, (ii) de novo peptide sequence tag extraction and its scoring, (iii) abundance weighted in silico spectral comparison, we further extended its horizon of capabilities by adding state-of-the-art algorithms for deconvolution and quantitation. Label free quantitation techniques are incorporated in first phase comprising of (i) Polynomial regression for missing peaks, (ii) spectral counting, a relative quantitation approach, (iii) extracted-ion chromatogram (XIC) used for simple peak detection thus quantitation. We have also taken its implementation from CPU to groundbreaking and emergent Graphical Processing Unit (GPU) technology. Further our aims include developing a top-down protein identification and quantitation engine implemented in the ASP.NET framework, which is a GPU based, open source, open architecture and publicly available web service that will use NVIDIA�s CUDA toolkit for implementing state-of-the-art algorithms for this purpose.

Download Link

Download Link