throughout this specification , the terms “ a ” and “ an ” and variations thereof represent the phrase “ at least one .” in all cases , the terms “ comprising ”, “ comprises ” and any other variations thereof should not be interpreted as being limitative to the elements listed thereafter . unless otherwise specified in the description , all words used herein carry their common meaning as understood by a person having ordinary skill in the art . in cases where examples are listed , it is to be understood that combinations of any of the alternative examples are also envisioned . the scope of the invention is not to be limited to the particular embodiments disclosed herein , which serve merely as examples representative of the limitations recited in the issued claims resulting from this application , and the equivalents of those limitations . polypeptides , proteins and / or potential drug targets (& gt ; 10 kda ) in general are magnitudes larger in molecular mass than small molecular chemical entities or drug candidates ( such as inhibitors , agonists , antagonists or modulators ) ( at around 500 but generally less than 1500 in molecular weight ) that may or may not have been found to possess biological effects on cells or organisms . detection of binding between polypeptides , proteins , or protein targets attached to solid surface and small molecular chemical entities are difficult due to relative small changes in response units ( ru ) as compared to ru changes typically observed for interactions that occur between molecules with larger mass ( such as polypeptide - polypeptide , protein - protein or dna - dna interactions ). detection of specific binding between a small molecular chemical entity and its cognate ( target ) polypeptide or protein among an array of hundreds or thousands of ( target or potential target ) polypeptides or proteins is even more difficult . alternatively , this target protein array / spr imaging system can be used to directly screen for compounds , ligands or polypeptides with affinity to any of the target proteins from a large collection of chemical , ligand or polypeptide libraries via an integrated autosampler . once their affinity is demonstrated , the hit compounds , ligands or polypeptide effectors may be further examined for their cellular activities ( e . g ., antibacterial , antifungal or antitumor activities ) according to the invention , a complete set of genes encoding target proteins for bacteria or other organisms / cell types ( such as tumor cells ) may be cloned and over - expressed with a variety of translational fusion tags to facilitate purification , analysis , and / or binding to solid surface of spr chips . these tags may be designed to fuse with either n - terminal , c - terminal , or both ends of the expressed protein . during construction of the target protein array , poly - histidine or poly - cystadine peptides of various lengths separated by zero or a predetermined number of “ spacer ” amino acids can be designed into the expression vector . glutathione s transferase ( gst ) tag sequences with an appropriate number of “ spacer ” amino acids may be designed into the expression vector into n - terminal , c - terminal , or both ends of the target protein . a custom target protein array can be constructed , which includes human homologous polypeptides or proteins to the bacterial essential target polypeptides or proteins ( whenever they exist and are available ) and the array can be used to determine the relative therapeutic index of a drug candidate or drug candidates ( i . e ., the best antibiotic drug candidate should bind its bacterial target protein with high affinity but bind to human counterpart poorly or not at all ). a custom target protein array can be constructed which includes tumor - specific target proteins as well as normal cell proteins to screen for anticancer agents with potent activity but little or no toxicity ( based on binding affinity to tumor - specific target vs . normal cell proteins ). for example , the human genome consists of 518 individual protein kinase genes ( kinome ) ( johnson and hunter , 2005 ), many of which are implicated in pathogenesis of cancer diseases . small molecule inhibitors have been discovered and / or developed into drugs or drug candidates for cancer diseases . an array of protein kinases in conjunction with spri may be used to identify additional cellular targets of drugs , drug candidates or lead compounds ( spectrum of activity ). alternatively , this kinome target protein array / spri system may be used to assess potential toxicity of drugs , drug candidates and lead compounds . the complete set of over - expressed essential proteins may be isolated and purified using metal chelator affinity chromatography or an equivalent method readily apparent to any person having ordinary skill in the art . these proteins may be arrayed ( using a microarrayer ) onto corresponding spr chips in relation to desired fusion tags to be used for binding . this target protein array may be analyzed using the spri technique with several known inhibitors ( e . g ., triclosan , phosphomycin , indolmycin and mupirocin for bacterial target protein array ) as qc ( quality control ) standards ( fig1 ). a solution of a single inhibitor ( or modulator ) or a mixture of compounds containing an inhibitory ( or effector ) ingredient ( such as a natural product extract ) whose cellular target is unknown flows through the chip surface and spr images of pre - flow and post - flow are compared and analyzed to identify interactions between the inhibitor ( or modulator ) and its target protein . since the exact positions and identities of all target proteins are known , the cellular target of the inhibitor is revealed . the most popular layout for achieving spr is the kretschmann configuration in which light passes through a p - polarizer and then enters a prism with high refractive index ( on which a thin layer of metal film is coated ) and impinges onto the back of the metal film ( on top of the metal film is the sample solution ). the reflected light beam is monitored as a reaction occurs at the metal film / solution interface . for spr imaging ( spri ), the light source is expanded and collimated to have a parallel light beam that irradiates a large area of the metal film through the prism . the reflected light beam is monitored by a ccd camera . a schematic representation of the instrumental set - up is shown in fig2 . other configurations are readily apparent . using the methods described herein , a target protein array / spri system may be used for various applications . for example , the system may be used to dereplicate a natural product extract which possesses a specific therapeutic activity but without knowledge of the identity of the active ingredient ( s ) and to eliminate an active natural product extract due to the presence of a known inhibitor . moreover , a target protein array / spri system can be used to screen directly for entities with affinity for one or more of the target proteins within the array from libraries of chemical compounds , ligands or polypeptides for lead discovery . other applications will be readily apparent to any person having ordinary skill in the art . other useful applications of the target protein array / spri system include , but are not limited to inclusion of homologous target proteins of a large number of bacterial species ( gram positive or gram negative ; anaerobic or aerobic species ) to determine in vitro a spectrum of activities of an antibacterial inhibitor , exploration of cellular metabolic relationships with known metabolites , signal molecules and modulators , and inclusion of multitudes of different therapeutic targets to screen for inhibitors , agonist or modulators . other applications include probing protein / protein interactions from cell or tissue extracts , inclusion of sequence - distinct therapeutic target proteins of different ethnic groups or individuals to evaluate drug toxicity or effectiveness among individuals of different genetic background ( pharmacogenomics ) prior to or post market launch of a therapeutic agent , discovery of new mechanisms of action or new indications of known drugs approved for a different indication or even a different disease category ( e . g ., a known antibiotic might be found to be an excellent anticancer agent ), and to identify cellular targets / additional targets of biologics drugs ( e . g ., monoclonal antibody drugs ), to determine the mechanisms of action or mechanisms of toxicity of these agents , or to discover tumor - specific antibodies randomly generated . we obtained over thirty clinical isolates of a . baumannii from nosocomial infections in new york city and los angeles . all of these isolates are multi - drug resistant ( i . e ., resistant to at least three antibiotics ) as depicted below . only antibiotics with breakpoints for a . baumannii were used . antibiotic abbreviations : amikacin ( amk ) cefepime ( fep ) cefotaxime ( ctx ) ceftazidime ( caz ) ceftriaxone ( cro ) ciprofloxacin ( cip ) doxycycline ( dox ) gatifloxacin ( gat ) gentamicin ( gen ) imipenem ( ipm ), levofloxacin ( lvx ) meropenem ( mem ) minocycline ( min ) piperacillin ( pip ) tetracycline ( tet ) tobramycin ( tob ). isolates la 01 to 20 were acquired from los angels county while ny - a to ny - h were obtained from new york city . strains aye and sdf are known multi - drug resistant strain and susceptible strain , respectively , and were acquired from france . strains 15869 , 17978 and 19606 were obtained from atcc . amk fep ctx caz cro cip dox gat gen ipm lvx mem min pip tet tob lac 01 s r r r r r s r r s i r s r r r lac 02 i r r r r r s r i i i r s r r r lac 03 i r r r r r s r r s r i s r r r lac 04 i i r r r r s s r s s s s r i r lac 05 r i i i i r s r r s r s s i r r lac 06 s s r s r r s s r s s s s s r s lac 07 r r r r r r s r r i r r s r r r lac 08 i i i i i r s r r s r s s i r r lac 09 r r r r r r s r r r r r s r r r lac 10 r r r r r r s r r r r r s r r r lac 11 s r r r r r r r r s r r r r r s lac 12 s r r r r r r r r s r s r r r s lac 13 s r r r r r r r i s r s r r r s lac 14 s r r r r r r r r s r s r r r s lac 15 r r r r r r s r i i r r s r r s lac 16 r r r r r r s r r i r s s r i r lac 17 i r r r r r s r r i r s s r r r lac 18 i r r r r r s r r i r s s r r r lac 19 r r r r r r s i r i i r s r i r lac 20 i r r r r r s r r i r i s r r r ny a i i r r r r s r r r i r s r i r ny b i r r r r r r r r r r r r r r r ny c r r r r r r s r r r r r s r r r ny d r r r r r r s r r r r r s r r r ny e s r r r i r r r r r r r i r r r ny f r r r r r r s r r r i r s r r r ny g s r r r r r r r s r r r s r r i ny h r r r r r r s r r r i r s r r r aye r r r r r r s i r r i s s r r r sdf s i s s i s s s s s s s s r i s 15839 r i r r r r r r r s r s s i r r 17978 s s s s s s s s s s s s s s s s 19606 s i i s i s s s r s s s s i i s antibiotic susceptibility profiles of clinical isolates of a . baumannii and reference strains . r , i , and s denote resistance , intermediate and susceptible , respectively . to determine if these clinical isolates of a . baumannii are clonally related and if there is correlation between phenotypic profiles ( antibiotic resistance ) and genetic profiles , chromosomal dna restriction digest analysis by pulse field gel electrophoresis was performed . results indicated that several la isolates are identical . for example , lac strains 7 , 9 and 10 are identical clonally ( see below ) and lac strains 16 , 17 , 18 , 19 and 20 are identical clonally ( data not shown ). genomic profiles of clinical isolates la 1 - 10 of a . baumannii genomic dnas were digested with apa i restriction enzyme , separated and visualized after pulse field gel electrophoresis . one striking similarity for all clinical isolates ( 20 from la , 8 from ny ) is that they all uniformly exhibited resistance phenotype to ciprofloxacin , a clinically used fluoroquinolone antibiotic . to determine their ciprofloxacin resistant determinants , dna sequences of both gyra and parc genes from these isolates ( except one ) were pcr amplified and sequenced . consistent with previous reports , all clinical isolates contain point mutations in the “ hot spots ” located within quinolone resistant determinant region in gyra and parc genes , rendering these isolates resistant to ciprofloxacin . using a flow injection spr ( fi - spr ), we were able to detect oligonucleotide hybridization at femtomolar level . we also demonstrated that the instrument is capable of detecting polynucleotides in real - samples ( e . g ., cdnas in arabidopsis thaliana leaf extract ). representative time - revolved spr signal corresponding to the detection of the apx - cs2 cdna , the spr signals at chips covered with probes containing single and six base mismatches , and the signal for the hybridization of a reference cdna ( actin cdna ) are respectively shown in curves a - d below . in both experiments , injections of a sample containing 33 pg / ml of total cdna were performed . curve c corresponds to the spr responses of a 35mer probe with 6 bases mismatching to the apx - cs2 gene and curve d is the sensorgram of the actin probe to the same cdna solution . the inset depicts the sensorgram similar to that of curve a , except that a more diluted cdna sample ( 3 . 3 pg / ml total dna ) was injected . as can be seen , when a six base - pair mismatches was present ( curve c ), essentially no binding or hybridization occurred ( i . e ., there was no change in the baseline signal after the injected sample elutes out of the flow cell ). when a single base - pair mismatch existed , the spr signal ( curve b ) decreased more than 50 % in comparison to that for the fully complementary duplex ( curve a ). these results suggest that the assay is highly specific and even single nucleotide polymorphism can be studied . the results also demonstrate that our instrument is highly sensitive , since the target cdna in a 3 . 3 pg / ml total cdna mixture could even be measured . such sensitivity is 4 - 5 orders of magnitude more sensitive than the rt - pcr of the same reaction . sensorgrams showing the detections with a 35mer apx - cs2 probe ( curve a ) and a 35mer probe with one mismatching base to the apx - cs2 gene ( curve b ). we recently applied spri to the analysis of dna / dna biomolecular interactions in an array format . we have demonstrated that specific binding of oligonucleotide dna molecules can be measured in an array format in real time ( see below ). “ a ” depicts four spots of oligonucleotide probes deposited onto a dextran - modified gold chip , with the two spots on the left corresponding to sequence specific to escherichia coli dna and the two spots on the right corresponding to enterrococcus faecium dna . when e . faecium specific target dna was injected , a greater thickness change was observed at the two spots on the right the sensor chip (“ b ”), suggesting that dna hybridization had taken place . when e . coli specific target dna was subsequently injected into the flow cell , the two spots on the left side of the chip become brighter (“ c ”). a spri image of a chip fabricated with oligonucleotide probes specific for e . coli ( left two spots ) and enterococcus faecium ( right two spots ); a differential spri image collected after e . coli species - specific target dna was injected in to the flow cell ; and ( c ) a differential spri image acquired after e . faecium specific target dna was injected into a flow cell . by injecting solutions containing different concentrations of fa and recording the resultant sensorgrams , the binding constant between fa and bsa was measured . the fact that protein binding of a small molecule compound such as fa can be measured again indicates that our instrument is highly sensitive . three different fa concentrations ( 10 , 20 , and 50 μm ) were injected . a flow rate of 1 ml / h was used . representative spr sensorgrams showing binding of ferulic acid ( structure on the left ) onto pre - immobilized bsa molecules . we have examined specific binding interactions between select target proteins and their specific inhibitors . our results indicated that spr can detect specific interactions between protein targets and their specific inhibitors . representative results of spr experiments are shown below . specific interaction between trps protein ( tryptophanyl trna synthetase ) and its known specific inhibitor indolmycin . dose - dependent specific binding between murg protein [ udp - n - acetylglucosamine - n - acetylmuramyl -( pentapeptide ) pyrophsosphoryl - undecaprenol n - acetylglucosamine transferase ] and its known inhibitor ramoplanin as determined by spr .