Indian Institute of Technology Bombay 4 articles published in JoVE Biochemistry "Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome Akul Naik1, Sanjeeva Srivastava1,2, Arun P. Wiita1,3,4 1Department of Laboratory Medicine, University of California, San Francisco, 2Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, 3Deptartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 4Chan Zuckerberg Biohub Here, we describe a proteomics workflow for characterization of the cell surface proteome of various cell types. This workflow includes cell surface protein enrichment, subsequent sample preparation, analysis using an LC-MS/MS platform, and data processing with specialized software. Biology Determination of the Mating Efficiency of Haploids in Saccharomyces cerevisiae Anjali Mahilkar*1,2, Prachitha Nagendra*1, Supreet Saini1 1Department of Chemical Engineering, Indian Institute of Technology Bombay, 2Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor In this work, a robust method for the quantification of mating efficiency in the yeast Saccharomyces cerevisiae is described. This method is particularly useful for the quantification of pre-zygotic barriers in speciation studies. Biology Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples Ayushi Verma*1, Vipin Kumar*1, Saicharan Ghantasala1, Shuvolina Mukherjee1, Sanjeeva Srivastava1 1Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay The described protocol provides an optimized quantitative proteomics analysis of tissue samples using two approaches: label-based and label free quantitation. Label-based approaches have the advantage of more accurate quantitation of proteins, while a label-free approach is more cost-effective and used to analyze hundreds of samples of a cohort. Biology Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue Saicharan Ghantasala*1, Medha Gayathri J Pai*2, Sanjeeva Srivastava2 1Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, 2Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay The protocol aims to introduce the use of a triple quadrupole mass spectrometer for Multiple Reaction Monitoring (MRM) of proteins from clinical samples. We have provided a systematic workflow starting from sample preparation to data analysis for clinical samples with all the necessary precautions to be taken.
