title: Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples.
abstract: 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.
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Geremy
authors.initials: G
authors.lastname: Clair
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Piehowski
authors.affiliation: Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35249, USA.
authors.forename: Teodora
authors.initials: T
authors.lastname: Nicola
authors.affiliation: Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Kitzmiller
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Eric L
authors.initials: EL
authors.lastname: Huang
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Erika M
authors.initials: EM
authors.lastname: Zink
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Ryan L
authors.initials: RL
authors.lastname: Sontag
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Orton
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.affiliation: Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Carson
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Whitsett
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Corley
authors.affiliation: Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35249, USA.
authors.forename: Namasivayam
authors.initials: N
authors.lastname: Ambalavanan
authors.affiliation: Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Ansong
mesh_terms: D000818:Animals; D000831:Animals, Newborn; D001331:Automation; D002851:Chromatography, High Pressure Liquid; D061346:Laser Capture Microdissection; D008168:Lung / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome