NanoLC-FT-ICR MS improves proteome coverage attainable for ~3000 laser microdissected breast carcinoma cells
Genomics and proteomics assays hold great promise for unrevealing molecular events that underlie human disease. Essential to this quest is the ability to effectively analyze clinical samples, but this task is considerably complicated by tissue heterogeneity. Laser capture microdissection (LCM) can be used to selectively isolate targeted cell populations (such as tumor cells) from their native tissue environment. However, the small number of cells that are typically procured by LCM severely limits the proteome coverage and biomarker discovery potential achievable by conventional proteomics platforms. Herein, we report on the use of a nano liquid chromatography-Fourier transform ion clyclotron resonance mass spectrometry (nLC-FTICR MS) platform for analyzing protein digests of approximately 3,000 LCM-derived tumor cells from breast carcinoma tissue, which corresponds to approximately 300 ng of total protein. A total of 2,836 peptides were identified by matching LC-MS data to accurate mass and time (AMT) tag databases that were previously established for the human mammary epithelium and several breast cancer cell lines. The peptide identifications correspond to 1,139 unique proteins confidently identified with 2 or more peptides. Based on categorization by Gene Ontology, identified proteins appear to cover a wide variety of biological functions and cellular compartments. This work demonstrates that a substantial number of proteins can be identified from a limited number of cells using the AMT tag approach and opens a door for high throughput in-depth proteomics analysis of clinical samples.
- Research Organization:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 899806
- Report Number(s):
- PNNL-SA-49906; 7190; KP1704020; TRN: US200708%%541
- Journal Information:
- Proteomics, 7(2):323-329, Journal Name: Proteomics, 7(2):323-329
- Country of Publication:
- United States
- Language:
- English
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