International Journal of Chemical Research, ISSN: 0975-3699, Volume 1, Issue 2, 2009, pp-08-17 Copyright © 2009, Bioinfo Publications, International Journal of Chemical Research, ISSN: 0975-3699, Volume 1, Issue 2, 2009 Protein analysis: progress of analytical techniques Ojha M.D. 1 , Bhandari P.A. 2 , Patil A.G. 3 , Prasade A.M. 4 1 I.C.L.E'S Motilal Jhunjhunwala College of Arts, Science and Commerce, Secytor-9, Vashi, Navi Mumbai 2 P.T.V.A’s Sathaye College, Vile Parle (E), Mumbai-400 057, India 3 V.E.S., College of Arts, Science and Commerce, Chembur, Mumbai-400 071, India 4 Gogate Jogalekar College of Science, Arts and Commerce, Ratnagiri, India Abstract- Protein analysis employs various techniques and methods, which help to study the protein. Quality Control (QC) is a system of routine technical activities, to measure and control the quality of the inventory as it is being developed. It provides routine and consistent checks to ensure data integrity, correctness, and completeness, helps to identify and address errors and omissions also document and archive inventory material and record all QC activities. Protein analysis techniques are developing fast due to the growing number of proteins obtained by recombinant DNA techniques. Keywords- Analytical techniques, DNA Chip, HPLC, LC-MS, GMP, BLAST Analytical techniques There are various number of modifications made in the existing techniques and instruments for more desirable analysis of proteins like, two LC- ESI–MS and CID-MS/MS methods been developed and validated for the determination of the novel oral 1,14 substituted taxane derivatives, IDN 5738 and IDN 5839, in mouse plasma. Sunfire C18 column was used for HPLC separation and the recovery was more than 90%. Using these methods for the first time the pharmacokinetics of the two taxanes was analyzed [1, 2]. HPLC has found immense application in pharmacokinetics. HPLC has been developed and validated for rapid determination of sinafloxacin, a novel fluoroquinolone in rat plasma using a fused-core C18-silica column. The total analysis time was as short as 3 min. The method was sensitive with a limit of detection (LOD) of 2 ng ml-1, with good linearity [3]. Liquid chromatography–mass spectrometry (LC-APCI- MS) has been used to analysed predominant triterpenes (free oleanolic acid, -sitosterol and - sitosterol-3-O--d-glucoside) in skin and cuticular wax of grape berries. The method showed good repeatibility. The grape varities which showed high variability was based triterpene content, quantitites of oleanolic acid of cuticular wax of the twelve analysed samples. The highest sitosterol and sitosterol glucoside content was also found in 'Othello' variety. This study on triterpenes could be an informative tool to characterize grape varieties [4]. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) using double-focusing sector field (LA-ICP-SFMS) or quadrupole-based mass spectrometers (LA-ICP- QMS) has been successfully applied as a powerful imaging (mapping) technique to produce quantitative images of detailed regionally specific element distributions in thin tissue sections of human or rodent brain. It was also applied to investigate metal distributions in plant and animal sections to study, the uptake and transport of nutrient and toxic elements or environmental contamination [5]. For diagnosis of various diseases and increasing survivability rates early detection of abnormal physiological conditions is required. Microfluidics-MS is being used as a very competitive technology for biomarker discovery. The integration of LC microchip devices with MS detection, to screen biomolecular marker MCF-7 in breast cancer .The potential of an LC-ESI-MS chip for comparative proteomic analysis of isotopically labeled MCF-7 breast cancer cell extracts is explored for the first time. [6]. The three- dimensional structures of proteins with a molecular weight up to 100 kDa, and solution structures of more than 100 plant proteins have been established by NMR spectroscopy. High- resolution NMR has become a key technology for the elucidation of biosynthetic pathways and metabolite flux via quantitative assessment of multiple isotopologues [7].High-performance liquid chromatography has been developed for determination of salicylaldehyde isonicotinoyl hydrazone(SIH) in rabbit plasma using C18 column This has provided the first information about the concentrations of SIH in plasma of a living subject. The results will have a significant impact on further progress in the development SIH [8]. Chip and array technology These are solid-phase ligand binding assay systems using immobilised proteins on surfaces which include glass, membranes, microtiter wells, mass spectrometer plates, and beads or other particles. These assays are highly parallel and often miniaturized. Their advantages include being rapid and automatable, capable of high sensitivity, economical on reagents, and giving an abundance of data for a single experiment. Bioinformatics support is important; the data handling demands sophisticated software and data comparison analysis. It has applications in diagnostics for detection of antigens and antibodies in blood samples; profiling of sera to discover new disease markers; environment and food monitoring, protein expression profiling, protein-protein interactions; ligand-binding