Large-scale quantitative clinical proteomics by label-free liquid chromatography and mass spectrometry.

We previously reported the development of an integrated proteome platform, namely 2-Dimensional Image Converted Analysis of Liquid chromatography and mass spectrometry (2DICAL), for quantitative comparison of large peptide datasets generated by nano-flow liquid chromatography (LC) and mass spectrometry (MS). The key technology of 2DICAL was the precise adjustment of the retention time of LC by dynamic programming. In order to apply 2DICAL to clinical studies that require comparison of a large number of patient samples we further refined the calculation algorithm and increased the accuracy and speed of the peptide peak alignment using a greedy algorithm, which had been used for fast DNA sequence alignment. The peptide peaks of each sample with the same m/z were extracted every 1 m/z and displayed with along the horizontal axis. Here we report a precise comparison of more than 150,000 typtic peptide ion peaks derived from 70 serum samples (40 patients with uterine endometrial cancer and 30 controls). The levels of 49 MS peaks were found to differ significantly between cancer patients and controls (P < 0.01, Welch's t-test and interquartile range [IQR] of >40), and the differential expression and identification of selected three proteins was validated by immunoblotting. 2DICAL was is highly advantageous for large-scale clinical proteomics because of its simple procedure, high throughput, and quantification accuracy.

Serum albumin-associated peptides of patients with uterine endometrial cancer.

The incidence of endometrial cancer is predicted to increase in developed countries. Because of the relatively high incidence of complications and low diagnostic sensitivity associated with endometrial tissue sampling, there is an urgent need for the development of a safe and non-invasive diagnostic method. The proteomic spectrum of albumin-associated peptides was obtained from a total of 125 serum samples (92 from endometrial cancer patients and 33 from controls) by matrix-assisted laser desorption/ionization hybrid quadrupole time-of-flight mass spectrometry, and the candidate markers were selected by the Mann-Whitney U-test and receiver operator characteristics analysis. We selected three mass peaks at 4769, 6254 and 11 792 m/z from a total of 507 peaks as distinguishing cancer patients from controls (P < 0.00001 and area under curve of over 0.8). When the cut-off points were defined as the averages of the values in the controls + 2 SD, the combination of the three peptides detected endometrial cancer with a sensitivity of 65.2% (60/92). Even stage I early endometrial cancers were detected with a sensitivity of 60.3% (38/63). Unfortunately, the three peptides were also detected in 44.6% (33/74) of myoma uteri patients, indicating that they are not specific to endometrial cancer. Although a large-scale study is necessary to confirm the clinical significance of the peptide biomarkers identified in this study, direct profiling of serum-albumin-bound peptides by high-resolution mass spectrometry was proven to have potential as a means of identifying biomarkers for a variety of diseases.

Preoperative diagnosis and treatment results in 106 patients with uterine sarcoma in Hokkaido, Japan.

OBJECTIVE: The aim of this study was to evaluate the clinicopathological features of uterine sarcoma in Hokkaido, Japan, between 1990 and 1999, and to identify prognostic factors of patients with such malignancies in this area and period. METHODS: One hundred and six patients with histologically proven uterine sarcoma were evaluated retrospectively. RESULTS: 93.5% of the patients with carcinosarcoma (CS) were diagnosed as having malignant disease preoperatively, while 65% of those with leiomyosarcoma (LMS) and 75% of those with endometrial stromal sarcoma (ESS) were preoperatively diagnosed as benign leiomyoma. When patients had no residual disease postoperatively, 5-year survival rates in patients with CS and LMS were 78.8 and 73.0%, respectively. ESS cases had a better prognosis (94.7% for stage I cases). In patients with early-stage sarcoma, pelvic lymphadenectomy and adjuvant chemotherapy, with or without cis-diamminedichloroplatinum, failed to show a survival benefit in both CS and LMS cases. Distant metastasis, myometrial invasion, and no residual disease at surgery were significantly associated with risk of death or recurrence in CS and LMS cases. CONCLUSION: Accurate preoperative diagnosis of uterine sarcoma was difficult, and no residual disease at surgery was the most important prognostic factor in patients with this disease. Postoperative adjuvant therapy had little effect on survival, especially in early-stage disease.