Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets
Abstract
Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution because of the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 μm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-μm-thick rat brain cortex tissue sections having diameters of 50, 100, and 200 μm, respectively. In conclusion, we also analyzed 100-μm-diameter sections corresponding to 10–18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression inmore »
- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1766614
- Alternate Identifier(s):
- OSTI ID: 1471240
- Report Number(s):
- PNNL-SA-138815
Journal ID: ISSN 1535-9476; S1535947620320636; PII: S1535947620320636
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Published Article
- Journal Name:
- Molecular and Cellular Proteomics
- Additional Journal Information:
- Journal Name: Molecular and Cellular Proteomics Journal Volume: 17 Journal Issue: 9; Journal ID: ISSN 1535-9476
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Zhu, Ying, Dou, Maowei, Piehowski, Paul D., Liang, Yiran, Wang, Fangjun, Chu, Rosalie K., Chrisler, William B., Smith, Jordan N., Schwarz, Kaitlynn C., Shen, Yufeng, Shukla, Anil K., Moore, Ronald J., Smith, Richard D., Qian, Wei-Jun, and Kelly, Ryan T. Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets. United States: N. p., 2018.
Web. doi:10.1074/mcp.TIR118.000686.
Zhu, Ying, Dou, Maowei, Piehowski, Paul D., Liang, Yiran, Wang, Fangjun, Chu, Rosalie K., Chrisler, William B., Smith, Jordan N., Schwarz, Kaitlynn C., Shen, Yufeng, Shukla, Anil K., Moore, Ronald J., Smith, Richard D., Qian, Wei-Jun, & Kelly, Ryan T. Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets. United States. https://doi.org/10.1074/mcp.TIR118.000686
Zhu, Ying, Dou, Maowei, Piehowski, Paul D., Liang, Yiran, Wang, Fangjun, Chu, Rosalie K., Chrisler, William B., Smith, Jordan N., Schwarz, Kaitlynn C., Shen, Yufeng, Shukla, Anil K., Moore, Ronald J., Smith, Richard D., Qian, Wei-Jun, and Kelly, Ryan T. Sat .
"Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets". United States. https://doi.org/10.1074/mcp.TIR118.000686.
@article{osti_1766614,
title = {Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets},
author = {Zhu, Ying and Dou, Maowei and Piehowski, Paul D. and Liang, Yiran and Wang, Fangjun and Chu, Rosalie K. and Chrisler, William B. and Smith, Jordan N. and Schwarz, Kaitlynn C. and Shen, Yufeng and Shukla, Anil K. and Moore, Ronald J. and Smith, Richard D. and Qian, Wei-Jun and Kelly, Ryan T.},
abstractNote = {Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution because of the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 μm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-μm-thick rat brain cortex tissue sections having diameters of 50, 100, and 200 μm, respectively. In conclusion, we also analyzed 100-μm-diameter sections corresponding to 10–18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues.},
doi = {10.1074/mcp.TIR118.000686},
journal = {Molecular and Cellular Proteomics},
number = 9,
volume = 17,
place = {United States},
year = {Sat Sep 01 00:00:00 EDT 2018},
month = {Sat Sep 01 00:00:00 EDT 2018}
}
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https://doi.org/10.1074/mcp.TIR118.000686
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Works referenced in this record:
Spatially-resolved protein surface microsampling from tissue sections using liquid extraction surface analysis
journal, April 2016
- Wisztorski, Maxence; Desmons, Annie; Quanico, Jusal
- PROTEOMICS, Vol. 16, Issue 11-12
Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module
journal, August 2016
- Deng, Liulin; Ibrahim, Yehia M.; Hamid, Ahmed M.
- Analytical Chemistry, Vol. 88, Issue 18
Sequential Operation Droplet Array: An Automated Microfluidic Platform for Picoliter-Scale Liquid Handling, Analysis, and Screening
journal, June 2013
- Zhu, Ying; Zhang, Yun-Xia; Cai, Long-Fei
- Analytical Chemistry, Vol. 85, Issue 14
High-Efficiency On-Line Solid-Phase Extraction Coupling to 15−150-μm-i.d. Column Liquid Chromatography for Proteomic Analysis
journal, July 2003
- Shen, Yufeng; Moore, Ronald J.; Zhao, Rui
- Analytical Chemistry, Vol. 75, Issue 14
Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping
journal, February 2015
- Van de Plas, Raf; Yang, Junhai; Spraggins, Jeffrey
- Nature Methods, Vol. 12, Issue 4
Calbindin D28K as a marker for the degeneration of the striatonigral pathway in Huntington's disease
journal, August 1990
- Kiyama, H.; Seto-Ohshima, A.; Emson, P. C.
- Brain Research, Vol. 525, Issue 2
Myelination of the Mouse Corpus Callosum
journal, November 1980
- Sturrock, R. R.
- Neuropathology and Applied Neurobiology, Vol. 6, Issue 6
Molecular imaging by mass spectrometry — looking beyond classical histology
journal, August 2010
- Schwamborn, Kristina; Caprioli, Richard M.
- Nature Reviews Cancer, Vol. 10, Issue 9
Tissue Imaging at Atmospheric Pressure Using Desorption Electrospray Ionization (DESI) Mass Spectrometry
journal, November 2006
- Wiseman, Justin M.; Ifa, Demian R.; Song, Qingyu
- Angewandte Chemie International Edition, Vol. 45, Issue 43
Online, Absolute Quantitation of Propranolol from Spatially Distinct 20- and 40-μm Dissections of Brain, Liver, and Kidney Thin Tissue Sections by Laser Microdissection–Liquid Vortex Capture–Mass Spectrometry
journal, May 2016
- Cahill, John F.; Kertesz, Vilmos; Weiskittel, Taylor M.
- Analytical Chemistry, Vol. 88, Issue 11
Spatially resolved transcriptomics and beyond
journal, December 2014
- Crosetto, Nicola; Bienko, Magda; van Oudenaarden, Alexander
- Nature Reviews Genetics, Vol. 16, Issue 1
Mass-spectrometric exploration of proteome structure and function
journal, September 2016
- Aebersold, Ruedi; Mann, Matthias
- Nature, Vol. 537, Issue 7620
Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections
journal, October 2017
- Dapic, Irena; Uwugiaren, Naomi; Jansen, Petra J.
- Analytical Chemistry, Vol. 89, Issue 20
Printing 2-Dimentional Droplet Array for Single-Cell Reverse Transcription Quantitative PCR Assay with a Microfluidic Robot
journal, April 2015
- Zhu, Ying; Zhang, Yun-Xia; Liu, Wen-Wen
- Scientific Reports, Vol. 5, Issue 1
Laser ablation sample transfer for localized LC-MS/MS proteomic analysis of tissue: LAST for LC-MS/MS proteomics
journal, March 2016
- Donnarumma, Fabrizio; Murray, Kermit K.
- Journal of Mass Spectrometry, Vol. 51, Issue 4
High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers
journal, July 2011
- Wiśniewski, Jacek R.; Ostasiewicz, Pawel; Mann, Matthias
- Journal of Proteome Research, Vol. 10, Issue 7
Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts
journal, September 2013
- Li, Shunqiang; Shen, Dong; Shao, Jieya
- Cell Reports, Vol. 4, Issue 6
Localized in Situ Hydrogel-Mediated Protein Digestion and Extraction Technique for on-Tissue Analysis
journal, February 2013
- Harris, Glenn A.; Nicklay, Joshua J.; Caprioli, Richard M.
- Analytical Chemistry, Vol. 85, Issue 5
The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing
journal, October 2017
- Lein, Ed; Borm, Lars E.; Linnarsson, Sten
- Science, Vol. 358, Issue 6359
Immunohistochemical localization of PDE10A in the rat brain
journal, September 2003
- Seeger, Thomas F.; Bartlett, Brenda; Coskran, Timothy M.
- Brain Research, Vol. 985, Issue 2
Enhanced Spatially Resolved Proteomics Using On-Tissue Hydrogel-Mediated Protein Digestion
journal, February 2017
- Rizzo, David G.; Prentice, Boone M.; Moore, Jessica L.
- Analytical Chemistry, Vol. 89, Issue 5
Set of Novel Automated Quantitative Microproteomics Protocols for Small Sample Amounts and Its Application to Kidney Tissue Substructures
journal, November 2016
- de Graaf, Erik Leonardus; Pellegrini, Davide; McDonnell, Liam A.
- Journal of Proteome Research, Vol. 15, Issue 12
Effects of endurance exercise on expressions of glial fibrillary acidic protein and myelin basic protein in developing rats with maternal infection-induced cerebral palsy
journal, February 2014
- Kim, Kijeong; Shin, Mal-Soon; Cho, Han-Sam
- Journal of Exercise Rehabilitation, Vol. 10, Issue 1
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
journal, December 2008
- Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A.
- Nature Protocols, Vol. 4, Issue 1
The Coming Age of Complete, Accurate, and Ubiquitous Proteomes
journal, February 2013
- Mann, Matthias; Kulak, Nils A.; Nagaraj, Nagarjuna
- Molecular Cell, Vol. 49, Issue 4
Spatial reconstruction of single-cell gene expression data
journal, April 2015
- Satija, Rahul; Farrell, Jeffrey A.; Gennert, David
- Nature Biotechnology, Vol. 33, Issue 5
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
journal, June 2016
- Ståhl, Patrik L.; Salmén, Fredrik; Vickovic, Sanja
- Science, Vol. 353, Issue 6294
Cell type– and brain region–resolved mouse brain proteome
journal, November 2015
- Sharma, Kirti; Schmitt, Sebastian; Bergner, Caroline G.
- Nature Neuroscience, Vol. 18, Issue 12
Advances in proteomics data analysis and display using an accurate mass and time tag approach
journal, January 2006
- Zimmer, Jennifer S. D.; Monroe, Matthew E.; Qian, Wei-Jun
- Mass Spectrometry Reviews, Vol. 25, Issue 3
Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples
journal, December 2016
- Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora
- Scientific Reports, Vol. 6, Issue 1
Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS
journal, January 2004
- Shen, Yufeng; Tolić, Nikola; Masselon, Christophe
- Analytical Chemistry, Vol. 76, Issue 1, p. 144-154
Analytical Properties of the Nanoelectrospray Ion Source
journal, January 1996
- Wilm, Matthias; Mann, Matthias
- Analytical Chemistry, Vol. 68, Issue 1
Universal sample preparation method for proteome analysis
journal, April 2009
- Wiśniewski, Jacek R.; Zougman, Alexandre; Nagaraj, Nagarjuna
- Nature Methods, Vol. 6, Issue 5
Fully Automated Four-Column Capillary LC−MS System for Maximizing Throughput in Proteomic Analyses
journal, January 2008
- Livesay, Eric A.; Tang, Keqi; Taylor, Beverley K.
- Analytical Chemistry, Vol. 80, Issue 1
2016 update of the PRIDE database and its related tools
journal, November 2015
- Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi
- Nucleic Acids Research, Vol. 44, Issue D1
Surface Modification of Poly(dimethylsiloxane) Using Ionic Complementary Peptides to Minimize Nonspecific Protein Adsorption
journal, May 2015
- Yu, Xiaoling; Xiao, Junzhu; Dang, Fuquan
- Langmuir, Vol. 31, Issue 21
Mass Spectrometry Imaging, Laser Capture Microdissection, and LC-MS/MS of the Same Tissue Section
journal, July 2017
- Dilillo, Marialaura; Pellegrini, Davide; Ait-Belkacem, Rima
- Journal of Proteome Research, Vol. 16, Issue 8
Enhancing bottom-up and top-down proteomic measurements with ion mobility separations
journal, July 2015
- Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.
- PROTEOMICS, Vol. 15, Issue 16
The Perseus computational platform for comprehensive analysis of (prote)omics data
journal, June 2016
- Tyanova, Stefka; Temu, Tikira; Sinitcyn, Pavel
- Nature Methods, Vol. 13, Issue 9
Ultrasensitive and Fast Bottom-up Analysis of Femtogram Amounts of Complex Proteome Digests
journal, October 2013
- Sun, Liangliang; Zhu, Guijie; Zhao, Yimeng
- Angewandte Chemie International Edition, Vol. 52, Issue 51
Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells
journal, February 2018
- Zhu, Ying; Piehowski, Paul D.; Zhao, Rui
- Nature Communications, Vol. 9, Issue 1
Integrated mass spectrometry imaging and omics workflows on the same tissue section using grid-aided, parafilm-assisted microdissection
journal, July 2017
- Quanico, Jusal; Franck, Julien; Wisztorski, Maxence
- Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1861, Issue 7
Utility of Accurate Mass Tags for Proteome-Wide Protein Identification
journal, July 2000
- Conrads, Thomas P.; Anderson, Gordon A.; Veenstra, Timothy D.
- Analytical Chemistry, Vol. 72, Issue 14
Ambient Mass Spectrometry Imaging Using Direct Liquid Extraction Techniques
journal, November 2015
- Laskin, Julia; Lanekoff, Ingela
- Analytical Chemistry, Vol. 88, Issue 1
Development of liquid microjunction extraction strategy for improving protein identification from tissue sections
journal, February 2013
- Quanico, Jusal; Franck, Julien; Dauly, Claire
- Journal of Proteomics, Vol. 79
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
journal, October 2016
- Tyanova, Stefka; Temu, Tikira; Cox, Juergen
- Nature Protocols, Vol. 11, Issue 12
NanoLC-MS coupling of liquid microjunction microextraction for on-tissue proteomic analysis
journal, July 2017
- Quanico, Jusal; Franck, Julien; Cardon, Tristan
- Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1865, Issue 7
An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood
journal, March 2015
- Li, Siyang; Plouffe, Brian D.; Belov, Arseniy M.
- Molecular & Cellular Proteomics, Vol. 14, Issue 6
Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples
journal, April 2018
- Zhu, Ying; Zhao, Rui; Piehowski, Paul D.
- International Journal of Mass Spectrometry, Vol. 427
Comparison of Extraction Methods for the Comprehensive Analysis of Mouse Brain Proteome using Shotgun-based Mass Spectrometry
journal, March 2012
- Shevchenko, Ganna; Musunuri, Sravani; Wetterhall, Magnus
- Journal of Proteome Research, Vol. 11, Issue 4