Serum and urine metabolite profiling reveals potential biomarkers of human hepatocellular carcinoma (MCP) (Posted 06/01/2011) Quantitative measurement and comparison of seven bile acids among benign liver tumor patients with liver cirrhosis and hepatitis, HCC patients with liver cirrhosis and hepatitis, HCC patients without liver cirrhosis and hepatitis, and healthy controls revealed that the abnormal levels of glycochenodeoxycholic acid, glycocholic acid, taurocholic acid, and chenodeoxycholic acid are associated with liver cirrhosis and hepatitis. ...
A filter aided sample preparation (FASP)-based method for the enrichment of glycopeptides (Posted 06/01/2010) N-linked glycosylation is a biologically important protein modification, but only a small fraction of modification sites have been mapped. We developed a "filter aided sample preparation" (FASP)-based method in which glycopeptides are enriched by binding to lectins on the top of a filter and mapped 6367 N-glycosylation sites on 2352 ...
Proteomics-Based Biomarkers in Chronic Obstructive Pulmonary Disease (Posted 05/16/2010) Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease associated with progressive obstruction of airflow affecting peripheral airways. The proteomic analysis highlights ways to identify novel biomarkers for diagnosis, therapy, and prognosis in COPD...
Autoantibodies against stress-induced phosphoprotein-1 as a novel biomarker candidate for ovarian cancer (Posted 05/16/2010) Detection of autoantibodies against tumor-associated antigens (TAA) has recently been shown to be a powerful tool for early detection of various cancers. The aim of this study was to investigate the possibility of using autoantibodies against TAA as novel biomarkers by a proteomics-based approach in patients with ovarian cancer. We used two-dimensional differential gel ...
Proteomic Analysis Reveals Virus-Specific Hsp25 Modulation in Cardiac Myocytes (Posted 03/19/2010) Viruses frequently infect the heart but clinical myocarditis is rare, suggesting that the cardiac antiviral response is uniquely effective. Indeed, the Type I interferon (IFN) response is cardiac cell-type specific and provides one integrated network of protection for the...
The most complete systems biology study of cancer stem cell (CSC) (Posted 03/07/2010) A glioblastoma stem cell (GSC) line, GSC11, grows as neurospheres in serum-free media supplemented with EGF (epidermal growth factor) and bFGF (basic fibroblast growth factor), and if implanted in nude mice brains, will recapitulate high-grade glial tumors....
Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells (Posted 03/07/2010) Histone deacetylases (HDACs) play critical roles in silencing tumor suppressor genes. HDAC inhibitors reactivate tumor suppressor genes and inhibit tumor cell growth in vitro and in vivo, and several HDAC inhibitors are currently being evaluated in clinical trials for cancer therapy. A comprehensive analysis of proteins regulated by HDAC ...
Proteomic biomarkers for the detection of diabetes or pre-diabetes (Posted 01/31/2010) Non-invasive methods are provided herein for the diagnosis of pre-diabetes and diabetes using biomarkers identified in a biological fluid, such as saliva. These biomarkers can be identified using...
MSQ: a tool for targeted quantitative proteomics platform (Posted 01/16/2010) Mass spectrometry (MS)-based quantitative proteomics has become a critical component of biological and clinical research for identification of biomarkers that can be used for early detection of diseases. In particular, MS-based targeted quantitative proteomics has been recently developed for the detection and validation of biomarker candidates in complex biological samples. ...
Empirical approach to false discovery rate estimation in shotgun proteomics (Posted 01/16/2010) " Estimation of false discovery rate (FDR) for identified peptides is an important step in large-scale proteomic studies. We introduced an empirical approach to the problem that is based on the FDR-like functions of sets of peptide spectral matches (PSMs). These functions have close values for equal-sized sets with the same FDR and depend ...
Ultrathroughput multiple reaction monitoring (UMRM) mass spectrometry (Posted 01/13/2010) A novel transformation of the multiplexing potential to the throughput potential of multiple reaction monitoring mass spectrometry is presented for targeted quantitation of proteins. Herein, this method is termed as ultrathroughput multiple reaction monitoring (UMRM) mass...
Ubiquitin as a biomarker for Creutzfeldt-Jakob disease (Posted 01/06/2010) Until today, a definite diagnosis of Creutzfeldt-Jakob disease (CJD) can only be made neuropathologically. At lifetime the early and differential diagnosis is often a problem. With SELDI we analyzed cerebrospinal fluid (CSF) from 32 CJD patients, 32 patients having other dementive diseases and 31 non-demented control ...
GTPases profiling by capture compound mass spectrometry (CCMS) (Posted 01/06/2010) The functional isolation of proteome subsets based on small molecule?protein interactions is an increasingly popular and promising field in functional proteomics. Entire protein families may be profiled on the basis of their common interaction with a metabolite or small molecule inhibitor. This is enabled by novel multifunctional small molecule probes...
Apolipoprotein A-I, Plasma retinol-binding protein, Gelsolin, and Vitamin D-binding protein as biomarkers for Klinefelter syndrome (Posted 01/06/2010) Klinefelter syndrome is a sex chromosomal abnormality (47, XXY karyotype), occurring approximately in 1 in 1000 male live births. In the present study proteomic analysis was performed in twelve 2nd trimester amniotic fluid samples, eight coming from pregnancies with normal males and four with Klinefelter syndrome foetuses, as shown by routine prenatal cytogenetic analysis. Samples were analysed by 2-DE, coupled with MALDI-TOF-MS analysis . Three...
High throughput MALDI imaging (Posted 01/06/2010) The term molecular histology has been used to convey the potential of imaging mass spectrometry to describe tissue by its constituent peptides and proteins, and to link this with established histological features. The low throughput of imaging mass spectrometry has been one of the factors inhibiting a full investigation of the clinical potential of molecular histology. Here we report the development of an automated set-up, consisting of a controlled environment ...
MRM assay using laser-microdissected paraffin-embedded tissues (Posted 01/06/2010) A preceding paper suggested 81 candidates of stage-specifically expressed proteins for either stage IA or IIIA by global shotgun proteomics and spectral counting. Six proteins, a subset of these proteins, were chosen for a further verification study since they are potentially soluble and/or secretory, which nature is convenient for detecting them in blood in clinical practice. The multiple-reaction monitoring (MRM) quantitative analysis suggested that napsin-A and anterior ...
Desmin phosphorylation as a biomarker for heart failure (Posted 12/12/2010) This invention relates to novel phosphorylation sites in the desmin protein that are associated with the onset of heart failure. The phosphorylation sites, i.e., Ser-27 and Ser-31, can be used as biomarkers
Detection and identification of post translationally modified peptides using a mass spectrometer (Posted 12/12/2010) A method of detecting and sequencing post translationally modified peptides is disclosed wherein a negative ion precursor scan (1) is performed. A negative ion high resolution MS scan (4) is then performed and then MRM channels in positive ion mode are determined and monitored (5). A positive ion MS/MS scan is then performed.
Ganglioside GM2 Activator Protein (GM2AP) as biomarker for acute renal failure (Posted 12/12/2010) The invention relates to a method of determining the risk of developing acute renal failure (ARF) in an individual, or of determining an ARF, and a method of predicting the progression of an ARF, by detecting and/or quantifying the protein Ganglioside GM2 Activator Protein (GM2AP).
A method increasing for efficiency of tandem mass spectrometry (Posted 12/12/2010) A system and method for performing MS/MS of everything are provided. Ionisable materials separated in order of molecular weight in a plurality of mass ranges are received at a mass spectrometer system in a given order in time, each mass range comprising a respective center mass value and a respective width.
A computer-implemented method for analyzing biomarkers in patients (Posted 12/12/2010) The present invention relates to computer-implemented methods and system for analysing a biomarker which cycles in a subject. In some other aspects, the present invention relates to analysing a biomarker which at least initially increases or decreases in amount in a subject following a treatment for a disease.
Phosphorylated troponin T as a biomarker for heart failure (Posted 12/12/2010) The present invention relates to methods and kits for the prediction of risk for heart failure using post-translation modified forms of cardiac troponin T as a biomarker.
Methods for capturing circulating biomarkers (Posted 06/17/2010) Methods, devices and systems for capturing biomarkers are provided. In particular, methods, compositions, and systems that utilize affinity capture devices comprising a processing chamber, affinity capture agent and porous membrane are provided.
Biomarkers for bipolar disorders (Posted 06/17/2010) The invention relates to a method of diagnosing or monitoring bipolar disorders, in particular bipolar I and bipolar II disorders
Lysozyme as a biomarker for atheroma (Posted 06/17/2010) The invention provides a method of diagnosing atheroma in an individual, the method comprising providing a sample from the individual, determining the level of lysozyme in the sample and assessing whether the level is indicative of atheroma in the individual
Stem cells from urine (Posted 06/17/2010) Provided herein are stem cells and methods for producing a culture of stem cells from urine. The stem cells may be differentiated into an osteogenic, chondrogenic, adipogenic, endothelial, neurogenic or myogenic lineage
Biomarkers for head and neck cancers (Posted 06/01/2010) A method of detecting the presence of specific human papilloma virus and host cell biomarkers associated with head and neck tumors in biological samples, like saliva, blood or biopsy tissue, obtained from a subject.
PlGF-2 and PlGF-3 as biomarkers for pre-eclampsia (Posted 06/01/2010) The present invention relates to a method for determining the risk of a pregnant woman developing pre-eclampsia. The method comprises i) determining the level of one or more biochemical markers in a sample obtained from a pregnant woman, and ii) comparing the level of the at least one biochemical marker
Method of de novo sequencing of peptide using the MALDI mass spectrometry (Posted 06/01/2010) The present invention relates to a method of peptide sequencing by MALDI (matrix-assisted laser desorption ionization) tandem mass spectrometry, which comprises the steps of chemically modifying a sample peptide with at least one chemical modification method selected from the group consisting
DNA encoding a hepcidin antimicrobial peptide (HAMP) allele for the diagnosis of oesophageal cancer (Posted 05/23/2010) A method of detecting a susceptibility to squamous-cell oesophageal carcinoma in a human subject, the method including the steps of obtaining from the subject a biological sample such as blood, plasma, serum and biopsy tissue which includes DNA encoding a hepcidin antimicrobial peptide
ABCC3 as a biomarker for chronic myeloid leukemia (CML) (Posted 05/23/2010) The present invention relates to a method of treating chronic myeloid leukemia (CML) in a human patient population. In particular, present invention relates to the use of ABCC3 as a biomarker for CML patients
ABCC3 as a biomarker for chronic myeloid leukemia patients (Posted 05/16/2010) The present invention relates to a method of treating chronic myeloid leukemia (CML) in a human patient population. In particular, present invention relates to the use of ABCC3 as a biomarker for CML patients
Mdogen-2 as a biomarker fro ovarian cancer (Posted 05/16/2010) Provided is a method of screening for, diagnosing or detecting ovarian cancer in a subject comprising (a) determining a level of mdogen-2 in a test sample from the subject, and (b) comparing the level of mdogen-2 in the test sample with a control, where detecting an increase in the level of mdogen-2 in the test sample compared to the control is indicative of ovarian cancer in the subject.
MALDI target plate utilizing micro-wells (Posted 05/11/2010) An arrangement for a MALDI sample plate for ion mass spectroscopy is disclosed. The sample is configured to shape the hypersonic explosion which creates the ions generated in a MALDI-type time-of-flight mass spectrometer. The MALDI sample plate includes a glass wafer formed from a plurality of clad glass fibers and has a first planar surface.
Method for the quantitation of percent glyeated protein in a biological sample suitable for use with a reflectance meter (Posted 05/11/2010) The present invention provides methods for quantitation of glycated protein in a biological sample using a solid support matrix by making a first bound protein measurement total bound protein under conditions where both glycated and non-glycated protein bind to the support in making a second bound protein measurement under conditions where glycated protein is bound to the support and non-glycated protein
Annexin A2 and S100A6 as biomarkers for acute tubular necrosis-related acute renal failure (Posted 04/03/2010) The present invention provides biomarkers for detecting kidney disease, selected from the oligonucleotide sequence, complementary sequence or derivatives, amino acid sequence or derivatives, fragment, variants, antibody of annexin A2 or S100A6 or combinations thereof
CTAP3 as a biomarker for ovarian cancer (Posted 04/03/2010) The present invention provides a protein-based biomarker that is useful in qualifying ovarian cancer status in a patient. In particular, the biomarker of this invention is useful to classify a subject sample as ovarian cancer or non-ovarian cancer. The biomarker can be detected by SELDI mass spectrometry
Akt and clusterin as biomarkers of chemotherapeutic responsiveness (Posted 03/19/2010) Compositions and methods for identifying cancers resistant to treatment due to the presence of elevated pAKT levels and/or overexpression of AKT. The methods comprise the detection
Biomarkers predictive of sensitivity or resistance to EGFR inhibitors such as gefitinib (Posted 03/19/2010) Disclosed is the identification, provision and use of biomarkers predictive of sensitivity or resistance to EGFR inhibitors such as gefitinib and products and processes related thereto. Specifically, a method is described for selecting a cancer patient who is predicted to benefit from
LCMS technology in vaccine development : by selective identification and characterization of immunogenic pathogen associated epitopes (Posted 03/19/2010) The present invention relates to an improved LCMS technology and its uses in methods for the selective identification and characterization of immunogenic pathogen associated epitopes, and the use thereof in vaccine development. One way of bridging the knowledge gap on T cell epitopes is to apply a new platform technology, ''immunoproteomics'', to directly assess the epitope display at the surface of antigen
Villin as a novel prostate biomarker (Posted 03/19/2010) The present invention relates to the filed of prostate cancer. Particularly, the invention relates to villin as a novel prostate biomarker. The invention further relates to compositions comprising anti-villin antibodies and use of these compositions for an improved detection of prostate cancer in a subject.
