Proteomics

Despite its enormous complexity, human plasma is still one of the most frequently used body fluids for identification and quantification of health and disease biomarkers. We have developed a new workflow for qualitative and quantitative analysis of human plasma proteins. The first step was to remove the seven most abundant...

Traditionally man has looked to nature to provide cures for diseases. This approach still exists today in the form of ‘bio-prospecting’ for therapeutically-active compounds in venoms. For example, the venoms of many reptiles offer a spectacular laboratory of bioactive molecules, including peptides and proteins. In the last 10–15 years, there...

A majority of extant life forms require O2 to survive and thrive. Oxidation is inevitably one of the most active cellular processes and one constant challenge that living organisms must face. Generation of oxidants including reactive oxygen species is a natural consequence of cellular metabolism of all biological systems during...

Several approaches have been described to identify proteins from MALDI MS/MS mass spectra. The sequence of tryptic peptides is determined by database searching or by de novo sequencing. Different algorithms are available to determine peptide sequence using mass spectra. False discovery of peptides is an associated problem with it. A...

Calcified aortic valve disease is a slowly progressive disorder that ranges from mild valve thickening with no obstruction of blood flow, known as aortic sclerosis, to severe calcification with impaired leaflet motion or aortic stenosis. In the present work we describe a rapid, reproducible and effective method to carry out...

Calcified aortic valve disease is a slowly progressive disorder that ranges from mild valve thickening with no obstruction of blood flow, known as aortic sclerosis, to severe calcification with impaired leaflet motion or aortic stenosis. In the present work we describe a rapid, reproducible and effective method to carry out...

Genomic islands interspersed in the chromosome of P. aeruginosa led to inter- and intraclonal diversity. Recently, a particular clone of P. aeruginosa called clone C was isolated from cystic fibrosis (CF) patients, clinical and non-clinical habitats throughout Europe and in Canada. P. aeruginosa clone C strains harbour up to several...

Traditionally, antibody-based assays, such as enzyme immunoassay (EIA), enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay (RIA), are the primary tool for the targeted quantification of a specific protein. An antibody-based assay can be run at high-throughput and has extraordinary sensitivity and specificity. In the cases where antibody-based assays exist, the process...

Since the function of the spinal cord depends on the proteins found there, better defying the normal Spinal Cord Proteome is an important and challenging task. Although brain and cerebrospinal fluid samples from patients with different central nervous system (CNS) disorders have been studied, a thorough examination of specific spinal...

This short note highlights a procedure to distinguish the residues having similar masses, oxidized methionine and phenylalanine containing peptides using MALDI TOF/TOF. The isotope intensities give a preliminary recognition of peptides containing oxidized methionine. In the peptides with partial oxidation of methionine a mass difference of 16 Da can be...

Proteomic discoveries are usually made using database searches for identification of proteins in a given protein sample derived from cells or tissues. High throughput searches leave a number of peptides not analyzed for a variety of reasons, such as posttranslational modification or a mutation that results changes in the peptide...

A Met residue is located adjacent to phosphorylation site 1 in the sequences of mitochondrial pyruvate dehydrogenase E1α subunits. When synthetic peptides including site 1 were treated with H2O2, the Met residue was oxidized to methionine sulfoxide (MetSO), and the peptides were no longer phosphorylated by E1α-kinase. Isolated mitochondria were...

G. Aravindhan1, R. Sathish Kumar2, K. Subha1, T.K.Subazini1, Alpana Dey3, Krishna Kant3 and G. Ramesh Kumar11Bioinformatics Division, AU-KBC Research Centre, MIT Campus, Anna University, Chennai—600 044, India. 2NRCFOSS, AU-KBC Research Centre, MIT Campus, Anna University, Chennai—600 044, India. 3Ministry of Communications and Information Technology, DT, New Delhi-110 003, India.AbstractAIM-BLAST, AJAX...

G. Aravindhan1, G. Ramesh Kumar1, R. Sathish Kumar2 and K. Subha11Bioinformatics Division, AU-KBC Research Centre, MIT Campus, Anna University, Chennai-600 044, India. 2NRCFOSS, AU-KBC Research Centre, MIT Campus, Anna University, Chennai-600 044, India.AbstractBioinformatics applications are generally multi-server dependants and will have to communicate several information repositories to carry out any...

Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological...

Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological...

Marcio L. Rodrigues1, Leonardo Nimrichter1, Debora L. Oliveira1, Joshua D. Nosanchuk2,3 and Arturo Casadevall2,3 1Laboratório de Estudos Integrados em Bioquímica Microbiana, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941590, Brazil. 2Department of Microbiology and Immunology and the 3Division of Infectious Diseases of the...

Mamoun Ahram1 and Emanuel F. Petricoin2 1Department of Pharmacology and Physiology, Faculty of Medicine, Mutah University, Mutah, Jordan. 2Center for Applied Proteomics and Molecular Medicine, George Mason University, Virginia, U.S.A. Abstract Recent technological developments in proteomics have shown promising initiatives in identifying novel biomarkers of various...

The rapidly expanding data sets derived from genomic and transcriptomic analyses have allowed greater understanding of structural and functional network patterns within the genome resulting in a realignment of thinking within a systems biologic framework of cancer. However, insofar as spatially and temporally dynamic differential gene expression at the protein...

Soyoung Ryu1,2, Byron Gallis1, Young Ah Goo1, Scott A. Shaffer1, Dragan Radulovic3, David R. Goodlett1 1Department of Medicinal Chemistry, University of Washington, Seattle, WA, U.S.A. 2Department of Statistics, University of Washington, Seattle, WA, U.S.A. 3Department of Mathematics, Florida Atlantic University, Boca Raton, FL, U.S.A. Abstract Recently, several research...

Hassan Dihazi Clinical Proteomics Laboratories, Nephrology and Rheumatology, Georg-August University Goettingen, Germany