Dr. Musharraf has over 100 research publications in reputed international journals. His current research is based on the utilization of modern mass spectrometric approaches as a powerful analytical tool in (1) proteomics and metabolomics studies for the search of bio-signatures in various cancers which are common in Pakistan, (2) screening and optimization of algal oil in Pakistani algae for biodiesel production, (3) development of protonated / deprotonated fragmentation pathways and structure fragmentation relationship (SFR) of pharmacologically significant classes of natural products, (4) MALDI matrix development for the analysis of metabolites in biological fluids and (5) LC- and GC-MS method development for marker compounds analysis in Pakistani agricultural products and commercially important plant extracts.