Geremy Clair 1 , Paul D. Piehowski 1 , Teodora Nicola 2 , Joseph A. Kitzmiller 3 , Eric L. Huang 1 , Erika M. Zink 1 , Ryan L. Sontag 1 , Daniel J. Orton 1 , Ronald J. Moore 1 , James P. Carson 4 , Richard D. Smith 1 , Jeffrey A. Whitsett 3 , Richard A. Corley 1 , Namasivayam Ambalavanan 2 , Charles Ansong a , 1
22 December 2016
Laser capture microdissection (LCM)-enabled region-specific tissue analyses are critical to better understand complex multicellular processes. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by LCM, impacting measurement robustness, quantification and throughput. Here, we coupled LCM with a proteomics workflow that provides fully automated analysis of proteomes from microdissected tissues. Benchmarking against the current state-of-the-art in ultrasensitive global proteomics (FASP workflow), our approach demonstrated significant improvements in quantification (~2-fold lower variance) and throughput (>5 times faster). Using our approach we for the first time characterized, to a depth of >3,400 proteins, the ontogeny of protein changes during normal lung development in microdissected alveolar tissue containing only 4,000 cells. Our analysis revealed seven defined modules of coordinated transcription factor-signaling molecule expression patterns, suggesting a complex network of temporal regulatory control directs normal lung development with epigenetic regulation fine-tuning pre-natal developmental processes.