Clinical proteomics using a large archive of formalin-fixed paraffinembedded (FFPE) tissue blocks has long been a challenge. Recently, a method for extracting proteins from FFPE tissue in the form of tryptic peptides was developed. Here we report the application of a highly sensitive mass spectrometry (MS)-based quantitative proteome method to a small amount of samples obtained by laser microdissection from FFPE tissues. Cancerous and adjacent normal epithelia were microdissected from FFPE tissue blocks of 10 squamous cell carcinomas of the tongue. Proteins were extracted in the form of tryptic peptides and analyzed by 2-dimensional image-converted analysis of liquid chromatography and mass spectrometry (2DICAL), a label-free quantitative proteomics method developed in our laboratory. From a total of 25 018 peaks we selected 72 mass peaks whose expression differed significantly between cancer and normal tissues (P < 0.001, paired t- S quamous cell carcinoma is the major histological type of oral cancer and develops in various anatomical locations within the oral cavity, including the tongue, bucca, oropharynx, gingiva, palate, lip, and floor of the mouth. Despite recent improvements in surgical techniques and chemo/radiotherapy, (1) the overall 5-year survival rate for patients with oral squamous cell carcinoma (OSCC) is still unsatisfactory.(2) OSCC has a propensity for rapid local invasion and spread (3) and is considered to be one of the most aggressive forms of squamous cell carcinoma of the head and neck region. Furthermore, the incidence of OSCC has been increasing among the young and middle-aged.(4-6) Therefore, there is an urgent need to develop new diagnostic and therapeutic modalities to improve the outcome of OSCC. Although there is considerable epidemiological evidence for a significant association of alcohol consumption, tobacco smoking, chronic mechanical stimulation, and betel quid chewing with the incidence of OSCC, the molecular mechanisms responsible for OSCC have not been fully elucidated. Overall gene expression in OSCC has been studied extensively over the past decade using microarray techniques. However, gene expression is not always correlated with the expression levels of the corresponding proteins.Although it is anticipated that protein expression reflects more directly the biological and pathological status of diseases, aberrations of protein expression during the course of oral carcinogenesis are largely unknown. Although the use of fresh material is desirable for any analytical technology, human tissue samples are not always available in sufficient quantity. Formalin-fixed paraffin-embedded (FFPE) tissue blocks are routinely preserved and stored after pathological diagnosis, and such archived material may provide an ample alternative resource for research purposes. However, FFPE specimens have usually not been used for proteomic analyses, as formaldehyde-induced intermolecular and intramolecular cross-linking hinders the solubility of proteins and complicates the extraction of intact ...

The development of a new plasma biomarker for early detection would be necessary to improve the overall outcome of colorectal cancer. Here we report the identification and validation of the ninth component of complement (C9) as a novel plasma biomarker for colorectal cancer by cutting-edge proteomic technologies. Plasma proteins were enzymatically digested into a large array of peptides, and the relative quantity of a total of 94 803 peptide peaks was compared between 31 colorectal cancer patients and 59 age/sex-matched healthy controls using 2D image-converted analysis of liquid chromatography and mass spectrometry. The selected biomarker candidates were validated in 345 subjects (115 colorectal cancer patients and 230 age/sex-matched healthy controls) using high-density reverse-phase protein microarrays. Plasma levels of Apo AI and C9 in colorectal cancer patients significantly differed from healthy controls with P values of 7.94 · 10 -4 and 1.43 · 10 -12 (Student's t-test), respectively. In particular, C9 was elevated in patients with colorectal cancer, including those with stage-I and -II diseases (P = 3.01 · 10 -3 and P = 1.13 · 10

Although the precise mechanism responsible for the correlation of haptoglobin with the future onset of hematologic toxicities remains to be clarified, our prediction model seems to have high practical utility for tailoring the treatment of patients receiving gemcitabine.

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. T he incidence and morbidity of endometrial cancer have been rising in Western countries and Japan. In 1970, endometrial cancer constituted only 3% of all uterine cancers, but the proportion had increased to 40% by 1998.(1) The contemporary human lifestyle is characterized by excessive fat consumption, obesity, physical inactivity, high energy intake, hypertension, and a high serum glucose concentration, which are risk factors for endometrial cancer, (2)(3)(4)(5)(6) and therefore its incidence is predicted to increase further. Abnormal uterine bleeding is the most frequent initial symptom of endometrial cancer, but many other disorders including endometriosis, metroptosis, myoma uteri, and uterine sarcoma can also produce this symptom. Endometrial cancer is usually diagnosed by histological examination of endometrial tissue. However, endometrial biopsy is often associated with complications such as infection, bleeding and perforation of the uterus, and the development of an alternative safe test is therefore necessary for diagnosis of endometrial cancer.The circulating serum proteome holds great promise as a reservoir of information that will be applicable for diagnosis of various diseases. Various gel-based and MS-based quantitative analyses of plasma/serum proteins have been conducted actively to identify serum biomarkers that can be applied to blood tests.(7-10) HPLC with a flow rate of the nanoliter-per-minute order coupled with high-speed MS/MS scanning has especially attracted considerable attention because of its comprehensive protein identification capacity.(11-13) However, MS/MS is essentially not a method for quantification, and several attempts have been made to provide a quantitative dimension to nano-LC-MS/MS. Semi-quantification is possible to some extent by counting the number of peptides sequenced. (14-16) To achieve more accurate quantification, several labeling methods have been developed, (17)(1...