NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells.

NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells.

Proteomics (2006-12-14)

Arzu Umar, Theo M Luider, John A Foekens, Ljiljana Pasa-Tolić

ABSTRACT

Proteomics assays hold great promise for unraveling molecular events that underlie human diseases. Effective analysis of clinical samples is essential, but this task is considerably complicated by tissue heterogeneity. Laser capture microdissection (LCM) can be used to selectively isolate target cells from their native tissue environment. However, the small number of cells that is typically procured by LCM severely limits proteome coverage and biomarker discovery potential achievable by conventional proteomics platforms. Herein, we describe the use of nanoLC-FT-ICR MS for analyzing protein digests of 3000 LCM-derived tumor cells from breast carcinoma tissue, corresponding to 300 ng of total protein. A total of 2282 peptides were identified by matching LC-MS data to accurate mass and time (AMT) tag databases that were previously established for human breast (cancer) cell lines. One thousand and three unique proteins were confidently identified with two or more peptides. Based on gene ontology categorization, 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 detected and identified from limited number of cells using the AMT tag approach, and opens doors for high-throughput in-depth proteomics analysis of clinical samples.

MATERIALS

Product Number

Brand

Product Description

EP951031208

Eppendorf^® Deepwell plates, DNA LoBind, 384 wells, white plate, conical bottom, colorless wells, capacity 200 μL, pack of 40 ea (5 bags × 8 plates)

EP022431005

Eppendorf^® DNA LoBind tubes, capacity 0.5 mL, PCR clean, pkg of 250 ea (5 x 50ea)

EP022431021

Eppendorf^® DNA LoBind tubes, capacity 1.5 mL, PCR clean, pkg of 250 ea (5 x 50ea)

EP951032085

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 40 ea (5 bags × 8 plates)

EP951040601

Eppendorf^® Protein LoBind Microplate 384/V-PP, PCR clean, V-bottom clear wells, white border, pack of 240 ea (10 bags × 24 plates)

EP951032409

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 120 ea (10 bags × 12 plates)

EP951031607

Eppendorf^® Deepwell plates, DNA LoBind, 384 wells, white plate, conical bottom, colorless wells, capacity 200 μL, pack of 120 ea (10 bags × 12 plates)

EP951032000

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 40 ea (5 bags × 8 plates)

EP022431048

Eppendorf^® DNA LoBind tubes, capacity 2.0 mL, PCR clean, pkg of 250 ea (5 x 50ea)

EP951032808

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 1000 μL, pkg of 120 ea (10 bags × 12 plates)

EP951032883

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 1000 μL, pkg of 120 ea (10 bags × 12 plates)

EP951033201

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 1000 μL, pkg of 80 ea (10 bags × 8 plates)

EP951033308

Eppendorf^® Deepwell plates, Protein LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 80 ea (10 bags × 8 plates)

EP022431064

Eppendorf^® Protein LoBind tubes, capacity 0.5 mL, PCR clean, pkg of 100 ea (2 x 50ea)

EP022431081

Eppendorf^® Protein LoBind tubes, capacity 1.5 mL, PCR clean, pkg of 100 ea (2 x 50ea)

EP022431102

Eppendorf^® Protein LoBind tubes, capacity 2.0 mL, PCR clean, pkg of 100 ea (2 x 50ea)

EP951032123

Eppendorf^® Deepwell plates, Protein LoBind, 96 wells, yellow plate, conical bottom, colorless wells, capacity 500 μL, pkg of 40 ea (5 bags × 8 plates)

EP951032921

Eppendorf^® Deepwell plates, Protein LoBind, 96 wells, yellow plate, conical bottom, colorless wells, capacity 500 μL, pkg of 20 ea (5 bags × 4 plates)