skip to main content

DOE PAGESDOE PAGES

Title: Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here in this paper, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.
Authors:
 [1] ; ORCiD logo [2] ;  [1] ; ORCiD logo [3] ;  [2] ;  [2] ;  [2] ; ORCiD logo [2] ;  [3] ;  [3] ; ORCiD logo [2] ; ORCiD logo [2] ; ORCiD logo [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
  3. Univ. of Florida, Gainesville, FL (United States). Dept. of Pathology, Immunology and Laboratory Medicine
Publication Date:
Report Number(s):
PNNL-SA-125235
Journal ID: ISSN 2041-1723; PII: 3367
Grant/Contract Number:
AC05-76RL01830; R21 EB020976; R33 CA225248; P41 GM103493; UC4 DK104167; DP3 DK110844; 1S10OD016350-01
Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
USDOE; National Institutes of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1432521