Patent Publication Number: US-2019187060-A1

Title: Continuous interleaved process for conducting an assay in a multi-well plate

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a division of U.S. patent application Ser. No. 12/422,081 filed Apr. 10, 2009 (now U.S. Pat. No. 10,203,286 issued Feb. 12, 2019), which claims the benefit of Application No. 61/123,975, filed Apr. 11, 2008. Reference is also made to Application No. 60/752,475, filed Dec. 21, 2005; Application No. 60/752,513, filed Dec. 21, 2005; application Ser. No. 11/642,970, filed Dec. 21, 2006; and application Ser. No. 11/642,968, filed Dec. 21, 2006. The disclosures of each of these applications are incorporated herein by reference in their entireties. 
    
    
     STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH 
     The U.S. Government has certain rights in this invention as provided for by the terms of contract HSHQDC-05-C-00037 and HSHQDC-06-00024 awarded by the Department of Homeland Security. 
    
    
     FIELD OF THE INVENTION 
     The invention relates to apparatuses, systems, methods, reagents, and kits for conducting assays. Certain embodiments of the apparatuses, systems, methods, reagents, and kits of the invention may be used for conducting automated sampling, sample preparation, and/or sample analysis in a multi-well plate assay format. For example, they may be used for automated analysis of particulates in air and/or liquid samples derived therefrom. 
     BACKGROUND OF THE INVENTION 
     Numerous methods and systems have been developed for conducting chemical, biochemical, and/or biological assays. These methods and systems are essential in a variety of applications including medical diagnostics, food and beverage testing, environmental monitoring, manufacturing quality control, drug discovery, and basic scientific research. Multi-well assay plates (also known as microtiter plates or microplates) have become a standard format for processing and analysis of multiple samples. Multi-well assay plates can take a variety of forms, sizes, and shapes. For convenience, some standards have appeared for instrumentation used to process samples for high-throughput assays. Multi-well assay plates typically are made in standard sizes and shapes, and have standard arrangements of wells. Arrangements of wells include those found in 96-well plates (12×8 array of wells), 384-well plates (24×16 array of wells), and 1536-well plates (48×32 array of wells). The Society for Biomolecular Screening has published recommended microplate specifications for a variety of plate formats (see http://www.sbsonline.org). 
     A variety of plate readers are available for conducting assay measurements in multi-well plates including readers that measure changes in optical absorbance, emission of luminescence (e.g., fluorescence, phosphorescence, chemiluminescence, and electrochemiluminescence), emission of radiation, changes in light scattering, and changes in a magnetic field. US 2004/0022677 and US 2005/0052646 of application Ser. Nos. 10/185,274 and 10/185,363, respectively, of Wohlstadter et al. describe solutions that are useful for carrying out singleplex and multiplex ECL assays in a multi-well plate format. They include plates that comprise a plate top with through-holes that form the walls of the wells and a plate bottom that is sealed against the plate top to form the bottom of the wells. The plate bottom has patterned conductive layers that provide the wells with electrode surfaces that act as both solid phase supports for binding reactions as well as electrodes for inducing electrochemiluminescence (ECL). The conductive layers may also include electrical contacts for applying electrical energy to the electrode surfaces. 
     Despite such known methods and systems for conducting assays, improved apparatuses, systems, methods, reagents, and kits for conducting automated sampling, sample preparation, and/or sample analysis in a multi-well plate assay format are needed. 
     SUMMARY OF THE INVENTION 
     Thus, the invention provides an apparatus for conducting luminescence assays in multi-well plates, the apparatus comprising (a) a light detection subsystem; (b) a liquid handling subsystem; and (c) a plate handling subsystem, wherein said apparatus processes assay samples by a continuous interleaved process. The apparatus may further comprise a sample-focused graphical user interface. 
     The apparatus of the present invention includes a plate handling subsystem that comprises:
         (a) a light-tight enclosure comprising:
           (i) one or more plate elevators with a plate lifting platform that can be raised and lowered;   (ii) a light-tight enclosure top having one or more plate introduction apertures positioned above said plate elevators and an imaging aperture, wherein said enclosure top comprises a sliding light-tight door for sealing said plate introduction apertures; and   (iii) a plate translation stage for translating a plate in one or more horizontal directions, wherein said stage comprises a plate carriage for supporting the plate, said plate carriage has an opening to allow said plate elevators positioned below the plate carriage to access and lift the plate, and said plate translation stage is configured to position plates below said imaging aperture and to position said plates above said plate elevators;   
           (b) one or more plate stackers mounted on said enclosure top, above said plate introduction apertures, wherein said plate stackers are configured to receive or deliver plates to said plate elevators; and   (c) a light detector mounted on said enclosure top and coupled to said imaging aperture with a light-tight seal.       

     The apparatus of the invention also includes a liquid handling subsystem that comprises a pipetting system for delivering liquids to or removing liquids from the wells of an assay plate in said apparatus. 
     In addition, the apparatus of the invention includes the following features:
         (a) a pipetting system that comprises a pipetting probe mounted on a pipette translation stage for translating said pipetting probe in a vertical direction and, optionally, in one or more horizontal directions;   (b) an enclosure top that has one or more pipetting apertures;   (c) a sliding light-tight door that has one or more pipetting apertures, wherein said sliding light-tight door has a pipetting position where said pipetting apertures in said enclosure top align with said pipetting apertures in said sliding light-tight door; and   (d) a pipette translation stage mounted on said enclosure top and configured to allow, when said sliding light-tight door is in said pipetting position, lowering said pipetting probe so as to access wells positioned under said pipetting apertures in said enclosure top.       

     The apparatus of the invention may further comprise a component selected from the group consisting of reagent and/or sample delivery station, reagent and/or sample tube rack, probe wash station, waste station, and combinations thereof, wherein said pipette translation stage is configured to move in one or more horizontal directions to access liquids in and/or deliver liquids to said component. Also included is a plate-seal piercing probe, wherein
         (i) said enclosure top has a piercing probe aperture;   (ii) said sliding light-tight door has a piercing probe aperture, wherein said sliding light-tight door has a piercing position where said piercing probe aperture in said enclosure top aligns with said piercing probe aperture in said sliding light-tight door; and   (iii) said piercing probe is mounted on said enclosure top and configured to allow, when said sliding light-tight door is in said piercing position, lowering said piercing probe so as to pierce seals on wells positioned under said piercing apertures in said enclosure top.       

     The apparatus of the invention includes a pipette translation stage that comprises a probe translation element and said pipette translation stage is configured to travel horizontally to contact said piercing probe with said probe translation element and to travel vertically to lower and raise said piercing probe with said probe translation element. 
     Further, the apparatus of the invention further comprising plate contacts for providing electrical energy to electrodes in wells positioned under said light detector. 
     The invention also provides a method for conducting an assay using the apparatus of described herein, wherein the method comprises:
         (a) introducing a multi-well plate to one of said plate stackers,   (b) sliding said sliding light-tight door so as to expose a plate introduction aperture under said one of said plate stackers,   (c) using one of said plate elevators to lower said plate from said one of said plate stackers to said plate carriage,   (d) sliding said sliding light-tight door to seal said plate introduction apertures,   (e) translating said plate carriage to position one or more wells under said light detector,   (e) detecting luminescence from said one or more wells,   (f) sliding said sliding light-tight door to expose at least one of said plate introduction apertures,   (g) translating said plate carriage to position said plate below said one of said plate introduction apertures, and   (h) raising one of said plate elevators to raise said plate to one of said plate stackers;       

     wherein said apparatus processes a plurality of wells in said multi-well plate in a continuous interleaved process. 
     The method described above may further comprise one or more of the following steps: pipetting sample and/or reagent into or out of one of said wells, removing seals from one or more of said wells, or applying electrical energy to electrodes in one or more of said wells. 
     The method of the invention further comprising the following steps in order:
         (a) pipetting sample and/or reagent into a first well of said multi-well plate;   (b) applying electrical energy to electrodes in said first well;   (c) translating said plate carriage to position said first well of said multi-well plate under said light detector;   (d) detecting luminescence from said first well; and repeating steps (a)-(d) on one or more additional wells of said multi-well plate after step (a) is completed on said first well.       

     The method of the invention may further comprise the following steps in order:
         (a) removing seals from one or more of said wells;   (b) pipetting sample and/or reagent into a first well of said multi-well plate;   (c) applying electrical energy to electrodes in said first well;   (d) translating said plate carriage to position said first well of said multi-well plate under said light detector;   (e) detecting luminescence from said first well;       

     and repeating steps (a)-(e) on one or more additional wells of said multi-well plate after step (a) is completed on said first well. 
     In one embodiment of the method of the present invention, the seal is removed in step (a) from said first well. 
     The invention also provides a method of conducting an assay using the apparatus of the invention wherein the method comprises:
         (a) introducing a plate to one of said plate stackers,   (b) sliding said sliding light-tight door so as to expose one of said plate introduction apertures,   (c) using one of said plate elevators to lower said plate from said one of said plate stackers to said plate carriage,   (d) sliding said sliding light-tight door to said piercing position,   (e) aligning a well of said plate under said piercing probe and piercing a seal on said well,   (f) sliding said sliding light-tight door to said pipetting position,   (g) using said pipetting probe to introduce and/or remove reagent and/or sample from one or more wells of said plate,   (h) sliding said sliding light-tight door to seal said plate introduction apertures,   (i) translating said plate carriage to position one or more wells under said light detector,   (j) detecting luminescence from said one or more wells,   (k) sliding said sliding light-tight door to expose one of said plate introduction apertures,   (l) translating said plate carriage to position said plate above one of said plate elevators, and   (m) raising said plate elevator to raise said plate to one of said plate stackers,       

     wherein said apparatus processes a plurality of wells in said multi-well plate in a continuous interleaved process. This method may further comprise one or more of the following steps:
             pipetting sample and/or reagent into or out of one of said wells,   removing seals from one or more of said wells, or   applying electrical energy to electrodes in one or more of said wells.           

     Accordingly, the method of the invention comprises the following steps in order:
         (a) pipetting sample and/or reagent(s) into a first well of said multi-well plate;   (b) applying electrical energy to electrodes in said first well;   (c) translating said plate carriage to position said first well of said multi-well plate under said light detector;   (d) detecting luminescence from said first well;       

     and repeating steps (a)-(d) on one or more additional wells of said multi-well plate after step (a) is completed on said first well. In one embodiment, the method comprises the following steps in order:
         (a) removing seals from one or more of said wells;   (b) pipetting sample and/or reagent(s) into a first well of said multi-well plate;   (c) applying electrical energy to electrodes in said first well;   (d) translating said plate carriage to position said first well of said multi-well plate under said light detector;   (e) detecting luminescence from said first well; and repeating steps (a)-(e) on one or more additional wells of said multi-well plate after step (a) is completed on said first well. Optionally, the seal is removed in step (a) from said first well.       

     In the method of the present invention, the light detector is an imaging system. For example, the imaging system is used to image luminescence from arrays of binding domains in said one or more wells and said apparatus reports luminescence values for luminescence emitted from individual elements of said arrays. 
     The method described herein may include a plate that comprises dry assay reagents, e.g., one or more wells comprise dry assay reagents that are sealed to protect the dry reagents from the environment. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  shows an assembled view of multi-well plate reader  100 . 
         FIG. 2  shows a view of plate reader  100  that exposes embodiments of the light detection and fluidic components. 
         FIG. 3  shows one embodiment of a light detection system  160  of plate reader  100 . 
         FIG. 4  shows embodiments of certain fluidic and seal piercing components. 
         FIG. 5  shows an embodiment of a sample/waste station  300 . 
         FIGS. 6 a -6 c    show an embodiment of a spring-loaded pipette probe  400 . 
         FIGS. 7 a -7 b    show an embodiment of a plate seal piercing probe  225 . 
         FIG. 8  shows an embodiment of an integrated plate seal piercer/pipettor  500 . 
         FIGS. 9 a -9 c    show top views of an embodiment of light-tight enclosure  110  of plate reader  100  and illustrates the operation of sliding light-tight door  150  (shown in cross-hatch). 
         FIG. 10  shows a view of the mechanical components present in one embodiment of light-tight enclosure  110  of plate reader  100 . 
         FIG. 11 a    shows a view of a cartridge used in multi-well plate reader  100  and  FIG. 11 b    is an expanded view of the components of one well of the cartridge. 
         FIG. 12  shows an overview of an assay protocol that may be used in the multi-well plate reader  100 . 
         FIGS. 13 a  and 13 b    are graphical representations of multi-well plate readers of the present invention. 
         FIGS. 14 a   -c are various graphical representations of one embodiment of a multi-well plate reader of the present invention.  FIG. 14 a    is a detailed overview of the instrument, whereas  FIG. 14 b    shows the instrument in an optional case.  FIG. 14 c    is an alternate view of the instrument in which the sample tube rack is replaced by a 96-multi-well plate. 
         FIGS. 15 a  and 15 b    are graphical representations of the top assembly of a multi-well plate reader of the present invention.  FIG. 15 a    shows the instrument in an optional case and  FIG. 15 b    shows a detailed view of the top assembly, which includes a pipetting probe capable of fluid-sensing and including two channels to prevent buffer contamination, an integrated tool for unsealing wells of an assay plate, a compact CCD camera and lens assembly, a plate stacker capable of holding up to five assay plates, and a bar code reader capable of reading and tracking assay plates in the input stack. 
         FIGS. 16 a  and 16 b    are graphical representations of the light-tight enclosure (LTE) used in one embodiment of the plate reader of the present invention.  FIG. 16 a    shows the instrument in an optional case and  FIG. 16 b    is a detailed view of the light-tight enclosure, which includes an X-Y table, elevator and contact mechanism. 
         FIGS. 17 a  and 17 b    are graphical representations of a sample station that may be used in one embodiment of the plate reader of the present invention. The sample station may include a linear guide which positions tubes under the pipettor, a permanent tube rack that can be used for samples or liquid reagents, a replaceable tube rack for 24 12×75 mm tubes or a 96-well source plate, and a waste container, which is optionally removable and optionally constructed of blow-molded plastic, capable of removal for waste disposal. The waste container also includes a pipette washing station to minimize sample carry-over. 
         FIG. 18  is a schematic overview of the sample interleaving process that may be used in the plate reader of the present invention.  FIGS. 19 a  and 19 b    show screenshots of alternative graphical user interfaces that may be used in connection with the plate reader of the present invention.  FIG. 19 a    shows a plate focused interface, whereas  FIG. 19 b    shows a sample queue focused interface. 
         FIG. 20  shows a screenshot of a graphical user interface that is sample queue focused. 
     
    
    
     DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION 
     The Detailed Description section provides descriptions of certain embodiments of the invention that should not be considered limiting but are intended to illustrate certain inventive aspects. 
     Described herein are apparatuses for conducting assays in a multi-well plate format that have one or more of the following desirable attributes: i) high sensitivity, ii) large dynamic range, iii) small size and weight, iv) array-based multiplexing capability, v) automated operation (including sample and/or reagent delivery); vi) ability to handle multiple plates, and vii) ability to handle sealed plates. We also describe components that are useful in such an apparatus, and methods for using such an apparatus and components. They are particularly well suited for, although not limited to, use for autonomous analysis of environmental, clinical, or food samples. The apparatus and methods may be used with a variety of assay detection techniques including, but not limited to, techniques measuring one or more detectable signals. Some of them are suitable for electrochemiluminescence measurements and, in particular, embodiments that are suitable for use with multi-well plates with integrated electrodes (and assay methods using these plates) such as those described in US 2004/0022677 and US 2005/0052646 of application Ser. Nos. 10/185,274 and 10/185,363, respectively, of Wohlstadter et al., and application Ser. No. 11/642,970 of Glezer et al. 
     An apparatus is provided for measuring a signal from wells of sealed multi-well assay plates comprising a) a seal removal tool for removing seals from wells of the multi-well plates, and b) a detection system for measuring the signal from wells of said multi-well plate. The seal removal tool may function by i) piercing sealing films with a probe with a seal piercing tip, ii) grabbing and removing caps on wells, iii) peeling sealing films from the tops of wells, or iv) removing the seal with a coring tool. 
     In one embodiment, the seal removal tool is a piercing probe that comprises i) a piercing section with external surfaces that taper to a vertex so as to form a piercing tip at one end of a piercing direction (the axis of translation during a piercing operation) and ii) a seal displacement section, arranged adjacent to the piercing section along the piercing direction. In certain specific embodiments, the seal displacement section has a cross-sectional shape, perpendicular to the piercing direction, that is selected to substantially conform to the shape of the openings of the wells on which the probe will operate. The probe may be slightly undersized relative to the well opening so as to allow the probe to slide into the well opening, and press or fold the pierced seal against the well walls. Such an approach may be used to remove the seal as a barrier to detecting assay signals in the well using detectors (for example, light detectors and/or light imaging systems) situated above the well. The appropriate clearance may be selected based on the thickness of a specific film and/or may be selected to be less than about 0.1 inches, less than about 0.2 inches, or less than about 0.3 inches. 
     In one example of a piercing tool, the cross-sectional shape of the seal displacement section is a circle. In another example, it is a square or a square with rounded corners. The piercing section may be conical in shape. Alternatively, it may include exposed cutting edges that, e.g., extend in a radial direction from the tip and can act to cut the seal during piercing and aid in reproducibly folding the seal against the well walls. In one specific example, the tip is pyramidal in shape, the edges of the pyramid providing exposed cutting edges. 
     In certain embodiments, the piercing probe is spring loaded such that the maximal downward force, along said piercing direction, of the probe on a plate seal is defined by the spring constant of a spring. The probe may also comprise a plate stop section adjacent to said seal displacement section that defines the maximum distance of travel of said piercing probe into said wells. In one specific example, the stop section is a region of the probe with a width that is too large to enter a well and the maximum distance is defined by the distance at which the stop section hits the top of the well. 
     The apparatus may further comprise a pipetting probe. In one embodiment, the piercing probe has a through-hole parallel to the piercing direction. The through-hole is, optionally, off-set from the piercing tip, and the pipetting probe is movably located in the through-hole such that it can be withdrawn into the piercing probe when the piercing probe is being used to remove a well seal and it can be extended from the piercing probe during pipetting operations. The piercing probe and pipetting probe may be controlled independently, e.g., by separate motors. Alternatively, one motor may be used to drive both probes. In one example, the piercing probe comprises a plate stop section as described above and the pipetting probe is coupled to the piercing probe by a spring. The spring is selected to have a spring constant such that i) when the probes are not exerting force on an object, the pipetting probe is withdrawn into the through-hole in the piercing probe, ii) translation of the pipetting probe toward a well results in the co-translation of the piercing probe and allows for the delivery of sufficient force to displace a seal on the well, and iii) continued translation past the maximal distance of travel of the piercing probe results in compression of the spring and extension of the pipetting probe from the piercing probe into said well where it may be used to pipette liquids into and out of the well. In an alternative embodiment, the pipetting probe is separate from the piercing proble and each are independently controlled. The pipetting probe may also include a fluid sensor. 
     A method is provided of using the apparatuses comprising seal removal tools (described above), the method comprising removing a seal from a well of a multi-well plate and detecting said signal from said well. Removing a seal may include piercing the seal on a well of a multi-well plate and, optionally, cutting the seal into sections (e.g., with using cutting edges on a piercing tip) and folding the sections against the internal walls of the well. The method may further include one or more of: pipetting a sample into the well, pipetting an assay reagent into the well, removing a liquid from the well, washing the well, illuminating the well, or applying an electrical potential to electrodes in the well. Additionally, the method may further comprise repeating some portion or all of the process described above on one or more additional wells of the plate. 
     Still further, the method may comprise conducting some portion or all of the processes described above on one or more wells in parallel. Thus, the apparatus can process more than one well of a multi-well plate at a time, e.g., up to ten wells or up to five wells, in parallel. Such parallel processing is referred to herein as sample interleaving and it is designed to increase sample throughput. 
     A reagent cartridge is provided which may be used to deliver reagent used by and store waste generated by a multi-well plate analysis apparatuses. According to one embodiment, a reagent cartridge comprises a cartridge body that encloses an internal volume. The cartridge body has a reagent port and a waste port for delivering reagent and receiving waste. The reagent cartridge also comprises reagent and waste compartments in the cartridge body that are connected, respectively, to the reagent and waste ports. The volume of the compartments are adjustable such that the relative proportion of the volume of the cartridge body occupied by reagent and waste can be adjusted, e.g., as reagent is consumed in assays and returned to the cartridge as waste. The total internal volume of the cartridge body may be less than about 2, less than about 1.75, less than about 1.5, or less than about 1.25 times the volume of liquid stored in the body, e.g., the volume of reagent originally provided in the cartridge, thus minimizing the space required for waste and reagent storage, and allowing for convenient one-step reagent replenishment and waste removal. In certain embodiments, the apparatus has a reagent cartridge slot configured to receive the cartridge, and provide fluidic connection to the waste and reagent ports, optionally via “push-to-connect” or “quick connect” fittings. 
     Optionally, the reagent and/or waste compartments are removable. In one embodiment, the reagent and/or waste compartments are removable and the apparatus further includes a sensor, e.g., an optical sensor, to monitor the fluid level(s) in the reagent and/or waste compartments. Once the reagent and/or waste compartments reach a certain minimal or maximal capacity, as detected by the sensor, the apparatus alerts the user to remove the reagent or waste compartment to replenish and/or empty the contents. In one embodiment, the motor of the pipetting probe is in communication with the sensor and when the reagent and/or waste compartments reach the minimal or maximal capacity, the pipetting probe motor is disabled by the apparatus, e.g., the probe sensor relays information regarding the capacity of the compartment to the instrument software, which then halts further pipetting action. 
     The reagent and waste compartments may be provided by collapsible bags located in the cartridge body. One of the reagent and waste compartments may be provided by a collapsible bag and the other may be provided by the cartridge body itself (i.e., the volume in the cartridge body excluding the volume defined by any collapsible bags in the cartridge body). In addition to the first reagent and waste compartments, the reagent cartridge may further comprise one or more additional collapsible reagent and/or waste compartments connected to one or more additional reagent and/or waste ports. Alternatively, one or the other of the reagent and waste compartments may be constructed from blow-molded plastic. 
     Methods of using the reagent cartridges are provided. The method comprises removing reagent from the reagent compartment and introducing waste into the waste compartment. In certain embodiments, at least about 70%, at least about 80%, or at least about 90% of the reagent volume is reintroduced into the reagent cartridge as waste. 
     Liquid dispensers are provided. The dispenser may be used to add or remove liquids from the wells of a multi-well plate. An assay apparatus is provided that includes the dispenser. One embodiment of the liquid dispenser comprises a pipetting probe comprising a vertical tube element. The dispenser also comprises a probe guide that supports the tube element in a vertical orientation, and configured to allow said tube element to move vertically in the guide between a fully extended position and a fully retracted position. The dispenser further comprises a spring element coupled to the vertical tube element and probe guide that biases the tube element to the fully extended position (i.e., extended downward). A vertical translation stage is attached to the probe guide to raise and lower the probe. 
     The tube element has a lower opening through which fluid is dispensed or aspirated. In one embodiment, the lower opening is a blunt tube end. Optionally, the end may be slotted to allow movement of fluid through the opening when the opening is pressed against a flat surface. In certain embodiments, the dispenser comprises two or more tube elements. In one specific example different reagents are dispensed through different tube elements. In another specific example, one tube element is used to dispense reagent and another tube element is used to aspirate waste. Multiple tube elements may be configured in a variety of arrangements, for example, as parallel tubes or concentric tubes. 
     A method is provided for using the liquid dispenser for adding or withdrawing fluid from a container, e.g., a well of a multi-well plate. One method comprises a) lowering the pipetting probe into the container by lowering the translation stage until the probe touches a bottom surface of the container, b) continuing to lower the translation stage such that said tube element pushes against the spring and retracts into the probe guide to a position between said fully extended and fully retracted positions, c) adding fluid to and/or withdrawing fluid from the container through the pipetting probe, and d) raising the pipetting probe out of said container by raising said translation stage. 
     In a specific embodiment employing a container with a piercable seal, the method may further comprise lowering the translation stage until the probe contacts and pierces the seal. In addition, piercing the seal may further comprise e) lowering the translation stage until the pipetting probe contacts the plate seal, f) continuing to lower the translation stage such that the tube element pushes against the spring and retracts in the probe guide to the fully retracted position, and g) continuing to lower the translation stage such that the pipetting probe pierces the plate seal and the tube element returns to the fully extended position. 
     An apparatus is provided for conducting luminescence assays in multi-well plates. One embodiment comprises a light-tight enclosure that provides a light-free environment in which luminescence measurements may be carried out. The enclosure includes a plate translation stage for translating a plate horizontally in the enclosure to zones where specific assay processing and/or detection steps are carried out. The enclosure also includes an enclosure top having one or more plate introduction apertures through which plates may be lowered onto or removed from the plate translation stage (manually or mechanically). A sliding light-tight door is used to seal the plate introduction apertures from environmental light prior to carrying out luminescence measurements. 
     The apparatus may also comprise a light detector which may be mounted within the light-tight enclosure or, alternatively, it may be mounted to a detection aperture on the enclosure top (e.g., via a light-tight connector or baffle). In certain embodiments, the light detector is an imaging light detector such as a CCD camera and may also include a lens. The apparatus may also comprise pipetting systems, seal piercing systems, reagent and waste storage containers, tube holders for sample or reagent tubes, fluidic stations for delivering/removing samples/reagents/waste, etc. These components may be conventional components such as components known in the art. Alternatively, the apparatus may employ specific components as described herein. Furthermore, the apparatus may comprise computers or other electronic systems for controlling operation the apparatus including, e.g., operating motorized mechanical systems, and triggering and/or analyzing luminescence signals. 
     Another embodiment of an apparatus for conducting luminescence assays in multi-well plates comprises a light-tight enclosure comprising i) one or more plate elevators having plate lifting platforms that can be raised and lowered, ii) a light-tight enclosure top having one or more plate introduction apertures positioned above the plate elevators and a detection aperture, the enclosure top comprising a sliding light-tight door for sealing the plate introduction apertures, and iii) a plate translation stage for translating a plate in one or more horizontal directions. The plate translation stage comprises a plate holder for supporting the plate which has an opening under the plate to allow plate elevators positioned below the plate holder to access and lift the plate. Furthermore, the plate translation stage being configured to position plates below the detection aperture and to position the plates above the plate elevators. 
     The apparatus further comprises one or more plate stackers and a light detector. The plate stackers are mounted on the enclosure top above the plate introduction apertures and are configured to receive plates from or deliver plates to the plate elevators. The light detector is mounted on the enclosure top and coupled to the imaging aperture with a light-tight seal. 
     Certain specific embodiments of the apparatus may further comprise a pipetting system for delivering liquids to or removing liquids from the wells of an assay plate in the apparatus. In one specific embodiment, the pipetting system comprises a pipetting probe mounted on a pipette translation stage for translating said pipetting probe in a vertical direction and, optionally, in one or more horizontal directions. Furthermore, the enclosure top has one or more pipetting apertures and the sliding light-tight door has one or more pipetting apertures. The sliding light-tight door has a pipetting position where the pipetting apertures in the enclosure top align with the pipetting apertures in the sliding light-tight door. The pipette translation stage is mounted on the enclosure top and configured such that, when the sliding light-tight door is in the pipetting position, the pipetting probe may be lowered to access wells positioned under the pipetting apertures in the enclosure top. 
     Another optional component of the apparatus is a seal removal tool such as a plate seal piercing probe. In one example, the enclosure top and sliding light-tight door have piercing probe apertures and the light-tight door has a piercing position where the piercing apertures in the door and top align. The piercing probe is mounted on the enclosure top and configured such that, when the sliding light-tight door is in the piercing position, the piercing probe may be lowered so as to pierce seals on wells positioned under the piercing apertures in the enclosure top. Advantageously, when both the piercing probe and the pipette probe are present, both may be driven with a single translation stage, e.g., as described above for the integrated pipetting/piercing tool. In an alternate embodiment, a pipette translation stage supporting the pipette probe comprises a probe translation element and the pipette translation stage is configured to travel horizontally and grab the piercing probe with the probe translation element, and to travel vertically to lower and raise said piercing probe. 
     Additional optional components of the apparatus are plate contacts for making electrical contact to the plates and providing electrical energy to electrodes in wells positioned under said light detector (e.g., for inducing ECL). 
     A method is also provided for using the apparatus for conducting luminescence assays in multi-well plates. The plates may be conventional multi-well plates. In certain embodiments, plates adapted for use in electrochemiluminescence assays are employed as described in application Ser. Nos. 10/185,274; 10/185,363; and 10/238,391. In assay methods that detect ECL from one well at a time, the electrode and electrode contacts in these wells are adapted to allow application of electrical energy to electrodes in only one well at a time. The apparatus my be particularly well-suited for carrying out assays in plates containing dry reagents and/or sealed wells, e.g., as described in application Ser. No. 11/642,970 of Glezer et al. 
     In one embodiment, the method comprises: a) introducing a plate to a plate stacker, b) opening the light-tight door, c) lower the plate from the plate stacker to the plate holder on the plate translation stage, d) sealing the light-tight door, e) translating the plate to position one or more wells under the light detector, e) detecting luminescence from the one or more wells, f) opening the light-tight door, g) translating the plate to a position under a plate stacker, and h) raising the plate to the plate stacker. The method may further comprising translating said plate carriage to position one or more additional wells under said light detector and detecting luminescence from said one or more additional wells. The method may also, optionally, comprise one or more of: i) pipetting sample/or reagent into or out of one of said wells, ii) removing seals from one or more of said wells, or iii) applying electrical energy to electrodes in one or more of said wells (e.g., to induce electrochemiluminescence). 
     Where the apparatus comprises a pipetting probe, and the enclosure top and sliding door includes pipetting apertures, the method may further comprise: sliding the sliding light-tight door to the pipetting position and using the pipetting probe to introduce and/or remove reagent and/or sample from one or more wells of the plate. Where the apparatus comprises a seal piercing probe, and the enclosure top and sliding door includes piercing apertures, the method may further comprise: sliding the sliding light-tight door to the piercing position, aligning a well of the plate under the piercing probe, and piercing a seal on the well. They may be repeated to pierce additional wells of the plate. In one embodiment, a seal on a well of a plate is pierced with the seal piercing tool prior to being accessed by a pipetting probe. In another embodiment, the well is first accessed by a pipetting probe (which pierces the seal to form one or more small holes or tears in the seal. The well is then subsequently pierced with the piercing probe to fully displace the seal and allow for unencumbered detection of signal from the well. 
     The light detector may be a conventional light detector such as a photodiode, avalanche photodiode, photomultiplier tube, or the like. Suitable light detectors also include arrays of such light detectors. Light detectors that may be used also include imaging systems such as CCD and CMOS cameras. The light detectors may also include lens, light guides, etc. for directing, focusing and/or imaging light on the detectors. In certain specific embodiments, an imaging system is used to image luminescence from arrays of binding domains in one or more wells of an assay plate and the assay apparatus reports luminescence values for luminescence emitted from individual elements of said arrays. 
     An environmental monitoring system is also provided that comprise an analyte detection module and an air sampling system. The air sampling system processes air to concentrate particulate matter in the air and suspend the particulates in a liquid suspension. The detection module is an apparatus for conducting luminescence assays in multi-well plates as disclosed herein. In operation, the air sampling system processes air for a certain period of time and delivers sample to the analyte detection module, which then carries out assays for one or more target analytes in one or more wells of an assay plate and, on completion of the assay, reports results. The air sampling system, detection module, and interface between the two components, preferably, is designed to operate in an autonomous fashion. At selected intervals of time, additional samples are delivered from the air sampling system to the detection module and analyzed in unused wells of the assay plate. The assays may be scheduled to be run in a serial fashion. Alternatively, the assays may be scheduled to be run in a staggered fashion in which some steps overlap. Through the use of multi-well plates (and plate stackers that hold multiple multi-well plates) long periods of autonomous operation can be achieved without requiring replenishment of consumables. 
       FIG. 1  shows an isometric view of one embodiment of multi-well plate reader  100 . Plate reader  100  has a light-tight enclosure  110  and a fluidic/imaging system enclosure  130 . Input and output plate stackers  122  and  120 , respectively, hold plates  105  for use in assays (plates are shown as having optional plate seals). Plate stackers  120  and  122  have plate release latches  125  that are spring loaded to allow plates raised from the light-tight enclosure below (using a plate elevator that is not shown in this view) to be captured in the stack. The latches in the input stack  122  can also be directed to be released to allow plates to be released from the stack to a plate elevator below (not shown). Window  140  provides an optical path for a bar code reader in fluidic/imaging system enclosure  130  to read bar codes on plates in input stacker  122 . Optionally, a plate stack cover (not shown) may be mounted over the plate stack to protect plates in the stacks from the environment. The plate stack cover may include heaters and/or coolers (e.g., a thermoelectric heater/cooler) and/or a desiccant chamber to maintain the plate stack under controlled temperature and/or humidity. 
       FIG. 2  is a view of plate reader  100  without the cover of fluidic/imaging system enclosure  130  and plates  105 . The view shows sliding light-tight door  150  which provides a light-tight seal to plate introduction apertures in the top of light-tight enclosure  100  located under plate stackers  120  and  122 . Motor  155  is coupled via belt to a linear screw drive (not shown) that opens door  150 . The views provided of plate reader  100  illustrate the use of certain specific translation mechanisms to move a variety of components of the apparatus including door  150 ; while the specific mechanisms chosen may have certain inventive advantages, the description is not meant to be limiting and one skilled in the art will be able to select from a variety of conventional single or multiple axis translation mechanisms. It should also be noted that to simplify the drawing, electronic circuit boards are not shown. 
     Imaging system  160  is mounted on an imaging aperture in the top of light-tight enclosure  110  and can image luminescence from plates in enclosure  110 . Pump  170  is used to drive fluids through the integrated pipetting system. One skilled in the art will be able to select appropriate pumps for use in the system including, but not limited to diaphragm pumps, peristaltic pumps, and syringe (or piston) pumps (as shown). Pump  170  also comprises a multi-port valve to allow the pump to push and pull fluids from different fluidic lines. Alternatively, multiple pumps can be used to independently control fluidics in different fluidic lines. A bar code reader  180  and rotating mirror  185  are used to scan bar codes from plates in input plate stacker  122 . Fluidic station  200  is used to deliver sample to the apparatus, wash the integrated pipettor, and dispose of waste from the pipettor. Piercing tool  225  is used to pierce and displace seals on wells of sealed plates so as to allow for unblocked imaging of the wells. Pipetting probe translation stage  250  provides horizontal and vertical translation of dual pipetting probe  260 . 
       FIG. 3  is another view of plate reader  100  that focuses on the components of imaging system  160  and shows camera  162  mounted on the top of light-tight enclosure  110  via camera bracket  164 . Lens  166 , coupled to camera  162 , is used to provide a focused image of luminescence generated from plates in enclosure  110 . Diaphragm  168  sealed to lens  166  and an aperture in the top of enclosure  110 , and allows imaging system  160  to image light from enclosure  110  while maintaining enclosure  110  in a light-tight environment protected from environmental light. Suitable cameras for use in imaging system  160  include, but are not limited to, conventional cameras such as film cameras, CCD cameras, CMOS cameras, and the like. CCD cameras may be cooled to lower electronic noise. Lens  166  is a high numerical aperture lens which may be made from glass or injection-molded plastic. The imaging system may be used to image one well or multiple wells of a plate at a time. The light collection efficiency for imaging light from a single well is higher than for imaging a group of wells due to the closer match in the size of the CCD chip and the area being imaged. The reduced size of the imaged area and the increase in collection efficiency allows for the use of small inexpensive CCD cameras and lenses while maintaining high sensitivity in detection. Particularly advantageous, for their low cost and size, is the use of non-cooled cameras or cameras with minimal cooling (preferably to about −20° C., about −10° C., about 0° C., or higher temperatures). 
       FIG. 4  shows enlarged views of plate seal piercing tool  225 , pipettor translation stage  250 , and sample/waste station  300 . Pipettor translation stage  250  comprises dual probe pipettor  260  which is mounted on motorized vertical translation stage  280  which is, in turn, mounted on horizontal translation stage  270 . Horizontal translation stage  270  uses a motor and belt drive to move vertical translation stage  280  along a linear guide rail, and moves pipettor  260  horizontally between piercing tool  225  and sample/waste station  300 . Vertical translation stage  280  uses motorized linear screw drive to raise and lower dual probe pipettor  260 . The range of motion allows probes  260  to access fluid in the sample/waste station and to access (through apertures in the top of light-tight enclosure  110 , not shown) wells of plates located in enclosure  110 . 
     Dual probe pipettor  260  includes fluidic connection for connecting both probes to fluidic lines. The use of two probes allows one probe to be used to deliver liquid to the wells and one probe to be used to remove waste. Alternatively, the two probes may be used to deliver to different reagents from two different fluidic lines. Vertical translation stage  280  includes piercing probe translation element  265  which is shaped to slide into slot  227  on piercing tool  225 . By using pipettor translation stage  270 , probe translation element may be moved so as to contact and grab piercing probe  225  at slot  227  via yoke  265 . Up and down movement of vertical stage  280  can then be used to control the vertical position of piercing probe  225 . 
       FIG. 5  shows two views of sample/waste station  300 . Station  300  has three open compartments defined on its upper surface: sample compartment  310 , waste compartment  320 , and washing compartment  330 . Sample compartment  310  is in fluidic connection with fluidic connector  312 . Sample delivered to fluidic connector  312  (e.g., from an air sampling system) fills sample compartment  310  and is made available to pipettor  260 . Waste compartment  320  drains to fluidic connector  322  and provides a receptacle for pipettor  260  to deliver waste. Washing compartment  330  can be used to wash the surface of pipettor  260 ; pipettor  260  is inserted in compartment  330  and the fluidic system is directed to dispense wash fluid which flows along the outside surface of pipettor  260  before overflowing into waste compartment  320 . Compartments  310 ,  320 , and  330  are countersunk into well  305  such that any overflow in compartments  310  and  330  is directed to waste and does not overflow station  300 . Fluidic sensors  314  and  324  are included to monitor fluid levels in compartments  310  and  320 , and ensure proper operation. Suitable fluid sensors include but are not limited to optical reflectance and capacitance sensors. 
     Reagent block  340  is simply used to provide a connection between an external liquid reagent source (connected to fluidic connector  344 ) and pump  170  (connected to fluidic connector  342 ). Reagent block  340  is monitored using fluid sensor  346  to ensure delivery of the liquid reagent. The liquid reagent may be omitted if not needed for a particular application. Non-exclusive examples of possible uses for the liquid reagent include use as a working fluid for the pump and fluid lines, as a wash buffer for washing assay wells, and/or as a read buffer for providing the optimal environment for luminescence measurements. In one embodiment, it is an electrochemiluminescence read buffer. Waste and liquid buffers may be stored in external or internal bottles. Alternatively, they may be stored in a reagent cartridge, e.g., as described herein. 
     One skilled in the art will understand that one or more of the functional components in sample/waste station  300  (e.g., one of the compartments, the reagent block, the sensors, etc.) may be omitted or may be provided in a separate part. In addition, the sample compartment may be complemented or replaced by other methods of providing samples. For example, a tube rack and/or source plate station may be incorporated in the instrument. Such embodiments may be configured so that the travel of probe  260  is sufficient to access such tubes or the wells of such source plates. The rack or plate holder may also have an axis of motion to help provide access to all tubes and wells. In one embodiment, the horizontal motion of the probe in the widthwise direction (i.e., from side to side relative to the base of the instrument) and movement of the tube or plate holder in the lengthwise direction (i.e., from front to back) provides access to arrays of tubes in a tube rack and/or wells held in a source plate in a plate holder. 
     In one embodiment, the apparatus includes a permanent sample rack which can accommodate test tubes for assay samples, reagents or both. The apparatus may also include a removable sample rack for test tubes, a multi-well plate or both. In one embodiment, the removable sample rack can accommodate at least 24 test tubes and/or a 96 well multi-well plate or a 96 deep well multi-well plate. The rack or plate holder may have a single axis of motion for moving the sample rack(s) fore and aft of the apparatus. In addition, dual probe pipettor,  260 , is of sufficient length to extend vertically the full depth of a test tube. 
       FIG. 6 a    shows a detailed view of a pipetting probe tip  400  which may be used on one or both of the probes on pipettor  260 . Probe  400  is a hollow tube with a blunt end with slots  410  cut into the tip around the circumference of the probe, allowing for fluid to be aspirating and dispensed from the probe when the probe is in contact with a surface. Rectangular slots are shown, but it is clear that alternative geometries, including triangular or semicircular openings, may also be used. There may be one or more slots around the circumference of the probe tip. The slots may be arranged in a symmetrical pattern, or the slots may be placed on a particular side of the probe (asymmetrical) so that liquid is aspirated from a preferred direction, i.e., in order to pull liquid from a meniscus around the bottom edge of the well. 
     Optionally, the pipetting probes used in the apparatuses are spring loaded so that they can contact a surface without damaging the surface or the probes.  FIGS. 6 b  and 6 c    show liquid dispenser  420  which shows an alternative probe embodiment that may be used. Liquid dispenser  420  comprises pipetting probe  424  having vertical tube element  425  and probe guide  430  that is configured to allows tube element  425  to move vertically in guide  430  between a fully extended position ( FIG. 6 b   ) and a fully retracted position ( FIG. 6 c   ). As shown, a large diameter region of probe  424  is confined between two position stops defined by inner surfaces of guide  430  although one skilled in the art will be able to design alternate configurations of position stops. Dispenser  420  also comprises spring element  440  which is compressed between a surface of guide  430  and ledge (or collar)  435  on vertical tube element  425  so that in the absence of external force on the bottom of the probe, said tube element stays in the extended position. The dispenser also comprises a vertical translation stage attached to guide  430  (not shown) that allows raising and lowering guide  430 . 
     In one embodiment of a pipetting operation using dispensor  420 , guide is lowered such that probe  424  is lowered into a container until it touches the bottom surface. Lowering continues such that tube element  425  pushes against spring  440 , and retracts into probe guide  430  to a position between the fully extended and fully retracted positions. Fluid is added or removed from the well and probe  424  is raised out of the well. In a specific example employing a container with a piercable seal, the method may further comprise lowering the translation stage until probe  424  contacts and pierces the seal. In addition, piercing the seal may further comprise e) lowering the translation stage until pipetting probe  424  contacts the plate seal, f) continuing to lower the translation stage such that the tube element  425  pushes against spring  440  and retracts into probe guide  430  to the fully retracted position, and g) continuing to lower the translation stage such that pipetting probe  424  pierces the plate seal and tube element  425  returns to the fully extended position. 
       FIGS. 7 a -7 b    show two views of piercing probe  225  from apparatus  100 . Piercing probe  225  comprises a piercing section  450  with external surfaces that taper to a vertex to form piercing tip  451  at one end of a piercing direction (the direction in which the probe moves to pierce a well, in this case the long axis of the probe). Piercing probe  225  also comprises a seal displacement section  452  arranged adjacent to piercing section  450  along the piercing dimension. 
     Displacement section  452  conforms to, but is slightly undersized, relative to the shape of the openings of the wells it is intended to pierce (in this case, square wells with rounded corners). After piercing section  450  pierces a seal, displacement section  452  pushes the plate seal against the well walls and prevents the seal from interfering with the detection of signals in the well. Piercing probe  225  also comprises plate stop section  454  adjacent to displacement section  452 . Stop section  454  is sized so that it can not enter the target wells and thus defines the maximal travel of probe  225  into a target well. 
     As noted above, displacement section  452  conforms to the shape of the wells it is intended to pierce. The cross-sectional area (perpendicular to the piercing direction) may take on any well shape including, but not limited to, round, elliptical, polygonal (regular or not), and polygonal with rounded corners. In one specific example it is square or square with rounded edges. Piercing section  450  may take on shapes that include, but are not limited to, conical shapes and pyramidal shapes. As shown in  FIG. 7 a   , it has a square pyramidal shape with edges  453  extending in a radial direction from tip  451 . The edges of the pyramid, advantageously, form cutting edges that help to cut a seal into sections during a piercing operation. For example, the piercing probe as shown in  FIGS. 7 a -7 b    is designed to pierce a seal on a rounded square well, cut the seal diagonally to form four triangular seal sections and fold these sections against the walls of the well. Cutting edges may also be raised from the surface, e.g., piercing system may be basically conical in shape but have raised cutting edges that extend from the conical surface. An apparatus is also provided for analyzing a multi-well plate that includes a piercing probe and a sealed plate. Suitable plates include plates sealed with a sealing film (for example, an adhesive, heat sealed, or sonic welded film). The film may comprise materials including, but not limited to, plastics and metal films or a combination of both. In one specific embodiment, the seal is a metal foil (which may be coated with a sealing layer such as heat sealable or adhesive coating or film) such as a heat sealable or adhesive aluminum foil. 
     As shown in  FIG. 7 b   , piercing probe  225  is spring loaded to provide a restorative force and to limit the maximum force that can be applied to a plate. Piercing probe  225  comprises a probe shaft  460  that slides within an aperture in probe guide  470 , probe guide  470  being fixedly mounted on the top of light tight enclosure  110  (see  FIG. 2 ). Compression spring  461  provides a restorative force that biases probe shaft  460  to be full raised into probe guide  470 . The restorative force is provided between i) pin  464  which is fixedly held in shaft  460  and ii) pin  462  which is fixedly held between guide  470  and the top of enclosure  110  but can move freely in slot  463  of shaft  460  (slot  463  defining the range of motion of probe shaft  460  relative to guide  470 ). Probe  225  is designed to be moved in the piercing direction by application of force to plunger  465  (for example, by grabbing slot  227  with probe displacement element  265  (see  FIG. 4 ) and translating probe displacement element  265  in a vertical direction). A second compression spring (not shown) between plunger  465  and pin  464  limits the force that may be applied with piercing probe  225 ; if excessive force is applied, the plunger will compress the second compression spring instead of moving shaft  460  relative to guide  470 . Pin  466  in slot  467  defines the maximal travel of plunger  465  in shaft  460 . 
       FIG. 8  shows alternate embodiments of piercing and pipetting probes that are integrated into one unit.  FIG. 8  shows a seal piercer/pipettor  500  that comprises a seal piercing probe  510  having a seal piercing section  520  with a seal piercing tip  521 , a seal displacement section  522 , and a plate stop section  524 . Piercer/pipettor  500  also comprises a piercing probe guide  540  having a cylindrical opening in which probe  510  can slide along the piercing direction. Piercing probe  510  also has a through-hole  525  parallel to the piercing direction and, in one example, off-set from piercing tip  521 . Pipette probe  530  is movably-located in through-hole  525  and fixedly attached to guide  540  such that movement of piercing probe  510  away from guide  540  causes pipetting probe  530  to extend from piercing probe  510 , and movement of piercing probe  510  toward guide  540  causes pipetting probe  530  to withdraw into piercing probe  510 . Compression spring  545  in guide  540  acts to push piercing probe  510  away from guide  540 , and to retract pipetting probe  530  (the maximal displacement of piercing probe  510  being limited by physical stops, specifically collar  526  on probe  510  and ledge  547  on guide  540 . 
     In operation, plate guide  540  is lowered toward a sealed well such that piercing probe  510  pierces and displaces the seal on the well. The spring constant of compression spring  545  is selected such that the seal can be pierced without substantial compression of spring  545  (and pipetting probe  530  remains retracted in through-hole  525  and co-translates with piercing probe  510 ). Continued lowering of guide  540  results in plate stop section  524  contacting the top surface of the well, preventing further translation of piercing probe  510 , and resulting in compression of spring  545  and extension of pipetting prove  530  into the well. 
       FIGS. 9 a -9 c    show top views of light-tight enclosure  110  of apparatus  100  (see  FIGS. 1-2 ) after removing most of the components mounted on top of enclosure  110 .  FIG. 9  shows three views (a-c) with sliding light-tight door  150  in three different positions (for clarity, exposed surfaces of door  150  are shown in cross-hatch). In  FIG. 9 a   , door  150  is in the fully sealed position so as to fully seal plate introduction apertures  626 , piercing probe aperture  630 , and pipetting probe apertures  640  in the top of enclosure  110 . Light detection aperture  610  is unblocked allowing detection and/or imaging of light emitted from wells positioned underneath aperture  610 . This view also shows plate contact mechanism  615  mounted on the bottom of enclosure  110  under aperture  610 . Plate contact mechanism  615  is designed for use with plates having electrodes within the wells and electrode contacts to these electrodes patterned on the bottom of the plates; plate contact mechanism  615  providing electrical contact to the electrode contacts of the wells positioned under aperture  610 . 
     In  FIG. 9 b   , sliding door  150  is partially opened to align piercing probe and pipetting probe apertures in sliding door  150  with corresponding apertures  630  and  640  in the top of enclosure  110 . With the door in this position, the piercing and pipetting probes can access wells positioned under the appropriate apertures. Multiple pipetting apertures are provided so that a pipetting probe can access multiple locations in a well or multiple wells in plate without repositioning the plate. In  FIG. 9 c   , sliding door  150  is fully opened, fully opening plate introduction apertures  626  and allowing the transfer of plates between plate stackers  120  and  122 , and plate elevator  625 . 
       FIG. 10  shows the mechanical components present in light-tight enclosure  110 . Plate translation stage  710  is mounted at an elevated position within enclosure  110 , and provides a plate holder  720  and holding plate  730 . Translation stage  710  comprises linear guides and motors that provide two horizontal axis of translation to plate holder  720 , and allows plate holder  720  to cover most of the horizontal area with enclosure  110 . Plate holder  720  supports plate  730  at the edges and is open in the center so that plate elevator  740  and contact mechanism  750  may contact the bottom of plate  730  through plate holder  720 . When plate holder  720  is positioned over one of platforms  745  on elevator  740 , the motor driven scissor mechanism of elevator  740  may operate to raise the platform, and lift plate  730  from plate holder  720  and up to a plate stacker mounted on the top of enclosure  110 . Similarly, when plate holder  720  is positioned over contact mechanism  750 , the motor driven scissor mechanism of contact mechanism  750  may operate to raise electrical contacts  755  so that they contact electrode contacts on the bottom of plate  730 , and allow application of electrical energy, through said contacts, to electrodes in the wells of plate  730 , for example, to induce electrochemiluminescence at those electrodes. It should be noted that the motion systems described for moving plates, electrical contacts, probes, etc. are not limited to the specific mechanisms depicted herein, although these mechanisms may have specific advantages. It is well within the purview of one in the art to select other conventional mechanism for accomplishing the desired movement of components. 
     In one embodiment, translation stage  710  may be used to achieve rapid one or two axis oscillation of plate holder  720  and, thereby, to shake and mix the contents of a plate on the plate holder. The shaking profiles can range from continuous single-axis shaking to duty-cycled orbital shaking. One example includes shaking with the axes at two different frequencies. The system may also provide for sonication to enhance mixing during sample incubation, for example, as described in the U.S. Pat. No. 6,413,783 of Wohlstadter et al. 
     In one embodiment, the light tight enclosure includes a light source located underneath the imaging aperture and below the elevation of the plate holder. This arrangement allows for the use of fiducial holes or windows in plates to be used to correct for errors in plate alignment. Light from the light source is passed through the fiducials and imaged on the imaging system so as to determine and correct for the alignment of the plate. Advantageously, plates formed from plate bottoms mated to a plate top (e.g., plates with screen printed plate bottoms mated to injection-molded plate tops as described in US 2004/0022677 and US 2005/0052646) advantageously include fiducials patterned (e.g., screen printed) or cut into the plate bottom to correct for misalignment of the plate bottom relative to the plate top. In one specific embodiment, the plate top on such a plate includes holes (e.g., in the outside frame of the plate top) aligned with fiducials on the plate bottom to allow imaging of the fiducials. Accordingly, the imaging of light generated under a plate may be used to communicate the exact position of the plate to the image processing software and also to provide for a camera focus check. The plate may then be realigned using a two-axis positioning system. Thus, a plate positioning method is provided comprising: (1) providing a plate having light-path openings; (2) illuminating plate from the bottom; (3) detecting light coming through light-path openings; and (4) optionally, realigning the plate. 
     The apparatus of the present invention uses multi-well assay plates such as those depicted in  FIG. 11 . One example of a multi-well plate is shown in  FIGS. 11 a    and  11   b,  which includes a foil plate seal over an injection-molded plate top and a screen-printed mylar plate bottom. The plate includes both assay wells and desiccant wells.  FIG. 11 b    provides an expanded view of one well of the assay plate. The plate bottom of the well includes a working electrode, a counter electrode and a dielectric layer. An array of materials, e.g., an array of antibodies specific for a target analyte, is attached to the working electrode and the wells include freeze-dried detection antibodies and/or positive controls for the assay on ledges above the plate bottom. An overview of the assay protocol using a plate such as that depicted in  FIG. 11  is shown schematically in  FIG. 12 . 
     Various embodiments of the apparatus of the present invention are contemplated herein.  FIG. 13  depicts two non-limiting examples.  FIG. 13 a    depicts a version of the apparatus which includes a detection component for air monitoring systems. The sample source for the apparatus in  FIG. 13 a    is fluid pumped into the sample station and the apparatus is capable of serial processing. Another embodiment is shown in  FIG. 13 b   .  FIG. 13 b    is capable of automated sample analysis, e.g., in the field laboratory setting, and it includes a sample rack holding tube queue or source plate. The embodiment shown in  FIG. 13 b    is capable of interleaved sample processing as described in more detail herein. 
       FIG. 14  is a detailed view of the apparatus depicted and generally described in  FIG. 13 b   . The apparatus in  FIG. 14 a    includes a permanent tube rack in addition to a replaceable sample tube rack. The permanent sample rack can accommodate a plurality of test tubes (and in the embodiment shown in  FIG. 14 a   , eight test tubes) that can be used for samples, reagents, or both. The removable sample rack can also accommodate a plurality of test tubes and/or multi-plate wells, e.g., up to 24 test tubes, a 96 well plate or a 96 deep well plate (this alternative arrangement is shown in  FIG. 14 c   ). In addition, the apparatus includes a sensor to detect which type of sample rack is installed in the apparatus. The apparatus in  FIG. 14  also includes a removable waste compartment and a fluid sensor in communication with the waste compartment. The waste compartment may be ejected by the waste cartridge release shown in  FIG. 14 a   . In an alternative embodiment, the waste compartment is externally positioned in the apparatus but in communication with the instrument and instrument software via a fluid pump that transports waste into the external waste compartment. The apparatus in  FIG. 14 b    also includes a sample access door, which includes, e.g., an LED light or other indicator or locking mechanism to prevent user access when the sample rack is in motion or otherwise inaccessible. In one embodiment, this mechanism includes a software controlled lock.  FIG. 15  depicts the top view of the apparatus shown in  FIG. 14 . 
       FIG. 16  provides a detailed view of the light-tight enclosure (LTE) used in the apparatus shown in  FIG. 14 . The LTE includes an X-Y table that can position a multi-well plate for transfer to the plate stack, well piercing, pipetting or ECL measurement stations within the apparatus. The LTE also includes an elevator to transfer a plate between the X-Y table and the input/output stacks, as well as a contact mechanism to make electrical contact to the electrodes in the plate well under the CCD camera. 
       FIG. 17  provides a detailed view of the sample station of the apparatus shown in  FIG. 14 . The sample station includes a linear guide to position tubes under the pipetting probe, permanent and replaceable tube racks, and a waste container. 
     As shown in  FIG. 18 , the present invention provides an apparatus for conducting luminescence assays in multi-well plates, the apparatus comprising (a) a light detection subsystem; (b) a liquid handling subsystem; and (c) a plate handling subsystem, wherein said apparatus processes assay samples by a continuous interleaved process. Thus, the invention further provides a method of using the apparatus of the present invention, wherein the process for an individual well comprises in series: 
     (a) a first sample addition phase (the “Front End” in the figure) wherein a pipetting probe is engaged in sample addition to the individual well, wherein the first sample addition phase comprises time slice n; 
     (b) a first incubation phase wherein the pipetting probe does not need to access and/or operate on the individual well but may, optionally, access and/or operate on other wells and the first incubation phase comprises time slice m; 
     (c) a first reagent addition phase (the “Back End” in the figure) wherein the pipetting probe is engaged in adding a reagent to the individual well (which may, optionally be part of a well washing step) and the first reagent addition phase comprises time slice p. 
     The first sample addition phase may also include seal piercing, reagent addition and other steps associated with preparing a well for an assay. The first reagent addition in the reagent addition phase may be part of a well washing step which may also include aspirating fluid from the individual well. The first reagent addition phase may also include carrying out a detection process on the individual well (e.g., inducing and measuring ECL from the individual well). Both the first sample addition and the first reagent addition phases may include steps for preparing or cleaning the pipetting probe (e.g., priming of washing of fluid lines, washing the pipette tip, etc.). 
     Optionally the process on an individual well may include additional incubation phases or reagent addition phases. For example and without limitation, a “two step” binding assay may include a second incubation phase and a second reagent addition phase. 
     The first well in a multi-well plate is subjected to steps (a)-(c) and these steps are repeated on one or more additional wells of the multi-well plate after step (a) is completed on the prior well. For example, once step (a) is completed on a first well of a plate, the first well is processed sequentially in steps (b)-(c). Once a step is completed on a well, that step may be completed on an additional well of the plate while the prior well proceeds to the next step. Likewise, the additional well is subjected to the remaining steps. The process may be carried out on each well on a plate, i.e., adjacent or contiguous wells on a plate, such that one well is subjected to a first step in the process (followed by the remaining steps in the process) and then the adjacent well is subjected to that step, followed by the subsequent steps in the process. Alternatively, the process may be carried out on wells that are not adjacent, i.e., one well is subjected to a first step in the process (followed by subsequent steps in the process) and then a distant well in the plate is subject to that step, followed by the subsequent steps in the process. 
     As shown in  FIG. 18 , one approach to measuring multiple samples is a serial sample process that involves completing sample analysis for one sample before beginning analysis on the next sample, a process that provides a low sample-throughput. To increase throughput, it is possible to begin processing for a sample during an incubation period for a previous sample, thus taking advantage of the fact that the pipettor is not needed for the previous sample during this time. One embodiment of such an approach is a continuous interleaved process includes dedicating alternating time slices to the different phases during which action is taken on individual wells (e.g., time slices n- and p, described above in phases (a) and(c)). During a dedicated sample addition time slice, the instrument will add sample to a well if a sample is available (and if no sample is available, the pipettor will sit idle for that time slice). Following the sample addition time slice, a reagent addition time slice will take place during which a well that has reached the end of an incubation phase will be processed (if no samples are incubating or if no samples have reached the end of their incubation phases, the pipettor will sit idle for that time slice). This alternating process of sample and reagent addition slices will then continue. A software scheduler tracks the status of all the assays running on a single plate by the apparatus at any given time. The scheduling approach described above ensures that all wells are processed using substantially the same assay protocol and timing while following a fairly simple scheduling algorithm. Alternatively, the software scheduler may be programmed to adjust one or more of the steps in the protocol, as determined by the user. During the interleaving process, shaking time for incubating samples is maximized such that the apparatus shakes the plate continuously unless the pipetting probe is accessing a well or an ECL signal is measured. 
     The interleaving process is beneficial in an apparatus comprising a single pipetting probe because it significantly enhances instrument throughput, particularly when the single probe is used to carry out multiple actions at different times in the assay process. The process is also beneficial in an apparatus comprising more than one pipetting probe. If more than one pipetting probe is employed, each probe may be assigned assay tasks for a given time slice and the assay steps may be further condensed, relative to a process carried out with a single pipetting probe. 
     In addition to increasing instrument throughput, sample interleaving facilitates the introduction of an automatic retest of a sample if an initial test has a signal that differs from a pre-defined threshold, e.g., the signal is higher or lower than the pre-defined threshold. For example, a sample may be subjected to an automatic retest if the mean or median signal from the various sample wells (typically an initial test well and at least one more retest well) exceeds the threshold for a particular assay. Alternatively, the program may require that all assays of a given sample must be positive for an overall “positive” call for the sample. 
       FIG. 19  shows two versions of the graphical user interface that may be used with the apparatus of the present invention. In the version depicted in  FIG. 19 a   , the user interface focuses on the assay plate, such that the user can review and visualize the plate and the assay results for each well in the plate as a whole. By contrast, the version shown in  FIG. 19 b    is sample focused. A sample focused user interface allows the user to enter sample information into the sample queue, e.g., sample names and rack locations, and the user can visualize the status of a given assay sample as well as assay results for each sample.  FIG. 20  provides yet another view of the sample focused graphical user interface. 
     The apparatuses, systems, method, reagents, and kits may be used for conducting assays on environmental samples. They may be particularly well-suited for conducting automated sampling, sample preparation, and analysis in the multi-well plate assay format. 
     One embodiment is an autonomous environmental monitoring system comprising (1) a sample collection module; (2) optionally, a sample processing module; and (3) a biological agent detection module, wherein the modules are fluidly connected, or in one example connectable, to allow for sample transfer between modules. According to one embodiment, an autonomous environmental system allows for multi-week periods of sustained operation requiring reduced human interaction. 
     The biological agents that may be detected include viral, bacterial, fungal, and parasitic pathogens as well as biological toxins. The agents themselves may be detected or they may be detected through measurement of materials derived from the agents including, but not limited to, cellular fragments, proteins, nucleic acids, lipids, polysaccharides, and toxins. 
     In one embodiment, the autonomous environmental monitoring system samples air, suspends particulate matter from the air sample in a collection fluid thereby creating a liquid sample, and performs an assay for one or more biological agents including viruses, bacteria, and toxins. The assay can be conducted in a singular or multiplexed assay format. 
     Some examples of biological agents include, but are not limited to, vaccinia virus,  Brucella  spp., botulinum toxin A, ricin,  Staphylococcal  enterotoxin B (SEB), Venezuelan equine encephalitis (VEE),  Yersinia pestis  (YP),  Bacillus anthracis  (BA),  Coxiella burnetii  (CB), and  Francisella tularensis  (FT) and combinations thereof. 
     In one embodiment, the system also comprises a computer that receives and processes data from a biological agent detection module. The computer recognizes in the data the positive identifications and, optionally, increases the frequency of conducting tests, transmits the data to alert the appropriate authorities, and further, optionally, automatically alerts nearby additional autonomous environmental monitoring system which automatically increase frequency of analysis and/or lower detection limits to identify presence of biological agents. 
     Thus, a network is also provided of autonomous environmental monitoring systems. According to one embodiment, each autonomous environmental monitoring system in the network may automatically determine individualized detection threshold limits by accounting for the background data at individual sites through acquiring sampling of the background at that specific location over the period of operation. The acquired background level information is used to track average background level and the standard deviations of the background level, and dynamically adjust the detection thresholds limit for a site location of an individual autonomous environmental monitoring system. 
     According to one embodiment, a sample collection module is capable of collecting and processing environmental samples such as suspensions of particles filtered, or otherwise concentrated, out of air samples. Air sampling systems that may be used include filter based collectors, impactors, virtual impactors, and wetted cyclones. Examples of standard sample collection modules that can be used include systems described in U.S. Pat. Nos. 6,888,085; 6,887,710; 6,867,044; and 6,567,008. Additionally, or alternatively, the sample collection module may be configured to collect, concentrate, and/or process other classes of samples such as water samples, soil samples, clinical samples, environmental swipes, etc., environmental sludges, food samples, beverages, samples that comprise suspensions of dirt, or biological samples. Clinical samples that may be analyzed include, but are not limited to, feces, mucosal swabs, physiological fluids , samples containing suspensions of cells, and combinations thereof. Specific examples of biological samples include blood, serum, plasma, tissue aspirates, tissue homogenates, cell cultures, cell culture supernatants (including cultures of eukaryotic and prokaryotic cells), urine, and cerebrospinal fluid. 
     A device for suspending particulate contained in the aerosolized particulate stream in a collection fluid may utilize a sonicator, a vortex mixer, a shaker, a simple mixer, or other means for optimizing contact between a fluid and an air sample. 
     According to one embodiment, a surfactant can be added to the collection fluid to prevent loss of biological agents to particles (including, but not limited to, paper, debris, and dust) in the collector solution. Useful surfactants include, but are not limited to ionic or non-ionic detergents or surfactants (e.g., classes of non-ionic detergents/surfactants are known by the trade names of BRIJ, TRITON, TWEEN, THESIT, LUBROL, GENAPOL, PLURONIC, TETRONIC, and SPAN). According to another embodiment, biological agents adsorbed on particulate, for example cellulose-based debris, are released back into solution by treatment with a carboxylic acid, for example, acetic acid, or citric acid. 
     According to one embodiment, detection of biological agents is improved by physical or chemical processing of the sample. The processing can be used to (1) concentrate biological agents in the sample, (2) lyse and/or fragment the biological agents, and (3) expose binding sites that would otherwise remain inaccessible. One or more processing steps may be included in the method of the present invention. 
     A device may include a concentrator system to concentrates biological agents suspended in the liquid sample by filtration, affinity separation and/or centrifugation. The filtration concentrator system may employ a filter selected to retain bacterial and viral particles while excising excess fluid. In one example, filtration concentrator system employs filters that retain biological molecules, such as proteins, toxins, nucleic acids, polysaccharides, and lipids. The system may also provide for biological agent removal from the filter and re-suspension in solution, for example by flowing buffer solution in the reverse direction and/or sonication. 
     The centrifugation concentrator system separates biological agents from the fluid by removing excess fluid following the centrifugation. The system also provides for re-suspension of the concentrated biological agents in a smaller volume of fluid following excess fluid removal. 
     According to one embodiment, the system employs affinity concentration unit comprising an affinity resin capable of binding to biological agents. Examples of the affinity resin include, but are not limited to, hydrophobic interaction resins (C4-C18, poly-, polyethyl-, and polymethyl-aspartamide). The resin can be conveniently packaged in columns, cartridges, or used as loose beads. The system provides for biological agent removal from the affinity media by elution with a release solvent. 
     According to one embodiment, at least one analyte can be concentrated through immobilization on the surface of at least one microparticle, or a plurality of microparticles (for example, a plurality of magnetically responsive microparticles), either passively (e.g., by non-specific binding) or via binding interactions with a binding partner of the analyte (e.g., an antibody that binds the analyte) or via chemical linkage such as via covalent bonds (e.g., reaction with an NETS-ester) and/or by reaction with an appropriate linker, or via one or more specific binding reagents, and/or by a combination thereof 
     In one embodiment, an ultrasonic lysis system is incorporated into the sample processing module, e.g., a system as described in U.S. Pat. No. 6,413,873 of Wohlstadter et al. Alternatively, the sample processing module may comprise a chemical lysis system. Chemical lysis by detergents, acids, bases, or other lysing agents can be used to break open vegetative bacteria, spores, and viral particles. An acidic or basic solution used for chemical lysis can then be neutralized prior to sample delivery to the analyte detection module. According to one embodiment, lysis system is incorporated upstream of a separator comprising a concentrator system. Alternatively, lysis follows removal of biological agents from a concentrator unit. 
     The sample processing module may further include a partial purification system, capable of removal of undesirable and in some examples interfering matter. For example, the partial purification system may include a filter permeable to biological molecules, but impervious to large particulate. The module may also include a chemical partial purification system (for example, a system for precipitating nucleic acids using alcohols). 
     According to one embodiment, a biological agent detection module comprises a reader for reading electrochemiluninescence (ECL) from multi-well plates. For example, ECL-based multiplexed testing is described in US 2004/0022677 and US 2004/0052646 of application Ser. Nos. 10/185,274 and 10/185,363, respectively; US 2003/0207290 of application Ser. No. 10/238,960; US 2003/0113713 of application Ser. No. 10/238,391; US 2004/0189311 of application Ser. No. 10/744,726; and US 2005/0142033 of application Ser. No. 10/980,198. 
     In one embodiment, the biological agent detection module has an integrated pipettor and a fluidic manifold for receiving samples and buffers, and distributing them to the wells of a plate. According to one preferred embodiment, the module allows the induction and measurement of ECL from only one well at a time. 
     One example of the analyte detection module, picture in  FIG. 1 , demonstrates the arrangement in a compact instrument of a mechanical system for storing and moving plates, a light detector for measuring luminescence (including ECL), a fluidic interface and pipetting system for transferring samples to the plates, and the electronic boards that drive the module. An alternative embodiment of such a module is depicted in  FIG. 14 . 
     According to one embodiment, the analyte detection module has three subsystems: (1) light detection, (2) liquid handling, and (3) plate handling. Each subsystem may, optionally, have a built-in error detection component to ensure reliable operation and to reduce the probability of false positives. 
     A method is also provided for conducting assays for biological agents including, but not limited to, biological warfare agents. In one embodiment, the method is a binding assay. In another embodiment, the method is a solid-phase binding assay (in one example, a solid phase immunoassay) and comprises contacting an assay composition with one or more binding surfaces that bind analytes of interest (or their binding competitors) present in the assay composition. The method may also include contacting the assay composition with one or more detection reagents capable of specifically binding with the analytes of interest. The multiplexed binding assay methods according to preferred embodiments can involve a number of formats available in the art. Suitable assay methods include sandwich or competitive binding assays format. Examples of sandwich immunoassays are described in U.S. Pat. Nos. 4,168,146 and 4,366,241. Examples of competitive immunoassays include those disclosed in U.S. Pat. Nos. 4,235,601; 4,442,204; and 5,208,535 to Buechler et al. In one example, small molecule toxins such as marine and fungal toxins can be advantageously measured in competitive immunoassay formats. 
     Binding reagents that can be used as detection reagents, the binding components of binding surfaces and/or bridging reagents include, but are not limited to, antibodies, receptors, ligands, haptens, antigens, epitopes, mimitopes, aptamers, hybridization partners, and intercalaters. Suitable binding reagent compositions include, but are not limited to, proteins, nucleic acids, drugs, steroids, hormones, lipids, polysaccharides, and combinations thereof. The term “antibody” includes intact antibody molecules (including hybrid antibodies assembled by in vitro re-association of antibody subunits), antibody fragments, and recombinant protein constructs comprising an antigen binding domain of an antibody (as described, e.g., in Porter &amp; Weir,  J. Cell Physiol.,  67 (Suppl 1):51-64, 1966; Hochman et al.,  Biochemistry  12:1130-1135, 1973). The term also includes intact antibody molecules, antibody fragments, and antibody constructs that have been chemically modified, e.g., by the introduction of a label. 
     Measured, as used herein, is understood to encompass quantitative and qualitative measurement, and encompasses measurements carried out for a variety of purposes including, but not limited to, detecting the presence of an analyte, quantitating the amount of an analyte, identifying a known analyte, and/or determining the identity of an unknown analyte in a sample. According to one embodiment, the amounts the first binding reagent and the second binding reagent bound to one or more binding surfaces may be presented as a concentration value of the analytes in a sample, i.e., the amount of each analyte per volume of sample. 
     Analytes may be detected using electrochemiluminescence-based assay formats. Electrochemiluminescence measurements are preferably carried out using binding reagents immobilized or otherwise collected on an electrode surface. Especially preferred electrodes include screen-printed carbon ink electrodes which may be patterned on the bottom of specially designed cartridges and/or multi-well plates (e.g., 24-, 96-, 384- etc. well plates). Electrochemiluminescence from ECL labels on the surface of the carbon electrodes is induced and measured using an imaging plate reader as described in US 2004/0022677 and US 2005/0052646. Analogous plates and plate readers are now commercially available (MULTI-SPOT® and MULTI-ARRAY® plates and SECTOR® instruments, Meso Scale Discovery, a division of Meso Scale Diagnostics, LLC, Gaithersburg, Md.). 
     In one embodiment, antibodies that are immobilized on the electrodes within the plates may be used to detect the selected biological agent in a sandwich immunoassay format. In another embodiment, microarrays of antibodies, patterned on integrated electrodes within the plates, will be used to detect the plurality of the selected biological agents in a sandwich immunoassay format. Accordingly, each well contains one or more capture antibodies immobilized on the working electrode of the plate and, optionally, in dry form, labeled detection antibodies and all additional reagents necessary for analysis of samples, and for carrying out positive and negative controls. In one example, arrays having multiple binding surfaces within a single well allow tests to be replicated to significantly reduce false positive identification. 
     A positive control method is provided to identify conditions or samples that may cause false negative measurements by interfering with the generation of signal. According to this aspect, positive control method comprises contacting sample with a binding reagent (e.g., an antibody) to a positive control substance (for example, to a non-toxic positive control substance) that is not expected to be observed in environmental samples; then contacting the sample with a labeled detection reagent (for example, an antibody) against the positive control substance and a controlled amount of the positive control substance, and measuring the signal. The positive control should, therefore, always provide a constant positive signal regardless of the sample. A significantly reduced signal may indicate that the sample interferes with the antibody binding reactions or the signal generating process, or may indicate a malfunction in the plate or instrument. 
     A negative control method is provided employing a capture reagent (e.g., an antibody) that is not matched with a detection reagent. The method comprises contacting a sample with a capture reagent in the presence of mismatched detection reagent and measuring signal. The negative control should, therefore, provide a negative signal regardless of the sample. A significantly elevated signal from the negative control indicates the presence of a material in the sample, such as a cross-linking agent, that is causing the non-specific binding of non-matched detection reagents to the negative control capture reagent. 
     A method is provided using a mixture of non-specific antibodies from the same species (e.g., polyclonal mouse, rabbit, goat, etc.) as specific capture antibodies to identify any non-specific binding effects that would otherwise provide false positive identification. This mixture may be selected to include the species of the antibodies used in the actual test measurements. 
     A method is provided using at least two different pairs of capture and detection reagents (e.g., antibodies) in alternating independently addressable wells to reduce the frequency of false positive identifications. Accordingly, the first binding reagent pair is used as a primary identification, which, if positive, triggers the confirmation test using the second binding reagent pair. The pairs may target the same marker or epitopes of a biological agent or, alternatively, they may further increase the orthogonality of the two measurements by targeting different markers or epitopes of a biological agent. An arrangement of at least two different antibody pairs in alternating well may be particularly advantageous. According to this aspect, the pairs are alternating as a primary identification set, thereby eliminating the need to dedicate wells as confirmation tests. Instead, if a sample is suspected to be positive based on the most recent test (based on either the first or the second pair), confirmation is simply performed by running the subsequent test well. 
     The reliability of detection method may be further improved by providing two or more different capture antibodies in a single well, wherein (a) the two or more different antibodies recognize the same marker and/or epitope of the same biological target; and/or b) the two or more different antibodies recognize different markers and/or epitopes of the same biological target. 
     One method for the detection of biological agents comprises (1) collecting an air sample using sample collection module (by the way of example, collecting aerosols in an air sample by using an integrated aerosol sampling system); (2) suspending the aerosols in a liquid; (3) optionally, transferring the aerosol suspension into a sample processing module; (4) optionally, concentrating and/or partially purifying the aerosol in the sample processing module (by the way of example, partially purifying by removing large particles); (5) transferring a liquid sample to a well of a multi-well plate, (6) adding at least one detection antibody against the same agents; (7) conducting an assay measurement and identifying samples that are positive for a biological agent; (8) optionally, performing a confirmation test by repeating (5)-(7); and (9) issuing an alert warning. Optionally, detection reagents are present in the wells in dry form and (6) may be omitted. In this case, addition of the sample results in reconstitution of the dried reagents. In one embodiment, step (5) includes transferring the sample to the well through the use of an integrated pipetting system. 
     Step (5) may comprise pumping the liquid sample into a sample chamber (e.g., sample compartment 310 of instrument 100) and using a pipetting system (e.g., probe 260 of instrument 100) to transfer the sample to a well of a plate), e.g., a plate in light-tight enclosure 110 of instrument 100). In one embodiment, instrument 100 as described above is used to carry out this operation as well as one or more (or all) of the subsequent analysis steps ((6)-(9)). 
     In one embodiment, the plate has an immobilized array of binding reagents (e.g., antibodies or nucleic acids) and bioagents in the sample bind to the corresponding immobilized reagent and a corresponding labeled detection reagent to form a sandwich complex. In some, the array is formed on an electrode and detection is carried out using an ECL measurement. In one embodiment, after addition of an ECL read buffer, labels on the electrode are induced to emit ECL by applying a voltage to the working electrode, and the emitted ECL is imaged with a CCD camera. Optionally, washing may be added prior to the ECL measurement to provide advantages in assay sensitivity, particularly for optically turbid samples generated by aerosol samplers in dirty environments. Image analysis is used to determine the location of the emitted light on the array and, thus, the identity of the agents in the sample. Image analysis also provides the intensity of the emitted light from each element of the antibody array and allows for precise quantitation of each bioagent. 
     Patents, patent applications, publications, and test methods cited in this disclosure are incorporated herein by reference in their entirety. 
     The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the claims. 
     A claim which recites “comprising” allows the inclusion of other elements to be within the scope of the claim; the invention is also described by such claims reciting the transitional phrases “consisting essentially of” (i.e., allowing the inclusion of other elements to be within the scope of the claim if they do not materially affect operation of the invention) or “consisting of” (i.e., allowing only the elements listed in the claim other than impurities or inconsequential activities which are ordinarily associated with the invention) instead of the “comprising” term. Any of these three transitions can be used to claim the invention.