[Frontiers in Bioscience E3, 1-10, January 1, 2011]
Biomarker discovery and identification from non-small cell lung cancer sera

Jie Du1, Shuan-ying Yang1, Xiu-li Lin1, Wen-li Shang1, Wei Zhang1, Shu-fen Huo1, Li-na Bu2, Wei Zhang3, Bin Zhou3, Yan-dong Nan1, Hua-dong Zheng1, Yan-feng Liu1

1Department of Respiratory Medicine, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China, 2Second Hospital of Xi'an, Xi'an, China, 3Department of General Thoracic Surgery, Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, China

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Materials and methods
3.1. Patients serum samples
3.2. Sample preparation and treatment with magnetic beads
3.3. Samples analyzed by MALDI-TOF
3.4. Differential peptides identification
3.5. Statistical Analysis
4. Result
4.1. System reproducibility
4.2. Unsupervised analysis of peptide ion signals from MS-based serum profiling differentiates NSCLC from controls.
4.3. Feature selection and model establishment
4.4. Identification of peaks of proteins by MS/MS
5. Discussion
6. Acknowledgements
7. References

1. ABSTRACT

Currently, serum biomarkers might usually be thought not to be used for early detection of lung cancer by some researchers. In this study, we used a highly optimized ClinProt-matrix-assisted laser desorption/ionization time-of flight mass spectrometer (MALDI-TOF-MS) to screen non-small cell lung carcinoma (NSCLC) markers in serum. A training set of spectra derived from 45 NSCLC patients, 24 patients with benign lung diseases (BLDs) and 21 healthy individuals, was used to develop a proteomic pattern that discriminated cancer from non-cancer effectively. A test set, including 74 cases (29 NSCLC patients and 45 controls), was used to validate this pattern. After cross-validation, the classifier showed sensitivity and specificity, 86.20% and 80.00%, respectively. Remarkably, 100% of early stage serum samples could be correctly classified as lung cancer. Furthermore, the differential peptides of 1865Da and 4209Da were identified as element of component 3 and eukaryotic peptide chain release factor GTP-binding subunit ERF, respectively. The patterns we described and peptides we identified may have clinical utility as surrogate markers for detection and classification of NSCLC.