EUROPEAN COMMISSION DIRECTORATE-GENERAL JOINT RESEARCH CENTRE Directorate D Institute for Reference Materials and Measurements Annex I Tender specifications Technical specifications for the supply of a Laser scanner based gel electrophoresis imager, including installation, validation, training, maintenance and related services.
1. Introduction Located in Geel, Belgium, the Institute for Reference Materials and Measurements (IRMM) is one of the seven institutes of the European Commission s Directorate General Joint Research Centre (JRC). The JRC s Institute for Reference Materials and Measurements (JRC-IRMM) brings and builds confidence in measurements, supports competitiveness and contributes to standardisation through its activities on harmonised testing methodologies, reference materials, pre-normative research, formal documentary standards and certification. JRC-IRMM second largest producer of matrix certified reference materials (CRM) worldwide and is the market leader in provision of Genetically Modified Organisms (GMO) reference materials. It is also an expert adviser in measurements related to food safety, quality and biotechnology, as well as a valued provider of reference measurement data. The institute currently employs over 250 staff working in multidisciplinary areas such as: aviation security, health diagnostics, food and feed safety and quality, advanced materials, nuclear safeguards, nuclear safety and security. JRC-IRMM currently operates four European Union Reference Laboratories in the area of food safety control. Further information on the IRMM and its activities, is available on the following website: https://ec.europa.eu/jrc/ 2. Defining the market Erro! Auto-referência de marcador inválida. 3. Subject of the market The instrument requested needs to be supplied to the Standards for Innovation and sustainable Development (SID) unit at JRC-IRMM. The laser scanner based imager will be employed for the characterisation of calibrants and protein based certified reference materials (CRMs) in terms of determination and evaluation of post-translational modifications (glycosylation, phosphorylation, isoforms ) as well as defining and assigning the measurand. Additionally, the laser scanner based system will be used to perform protein impurities identification and assessment. The instrument will also serve to perform comparative studies to address processing and formulation effect on the CRMs (stability, denaturation, modifications ). Multiplexing analyses for the detection and value assignment of several measurands in CRMs with the 2D DIGE (2-D Fluorescence Difference Gel Electrophoresis) technology will also be tackled with the requested instrument. Technical specifications Supply Laser scanner imager 2
4. Minimum technical requirements The tenders must fully comply with the following minimum technical specifications: Minimum technical requirements Compliance check Page in your offer (if applicable) 4.1 Laser scanner imager Robust and compact benchtop instrument. Modular to allow upgrades with new features. Laser based instrument: the system shall be able to house 4 lasers simultaneously. Instrument shall possess 4 solid state lasers for excitation: blue laser (473-488 nm) green laser (532 nm) red laser (635 nm) near infra red laser (685-785 nm) to cover the highest wavelength range possible for the detection. The detectors should allow equivalent signal detection along the complete wavelength range. High flexibility: Easy exchange of lasers to allow addressing future applications and using many different fluorophores without engineer intervention. Modular access to the optical components. The system shall have Negligible Crosstalks thanks to: Filters with low bandwidth 25 nm to optimise signal to noise ratios over the wavelength range (from visible up to NIR) for multi-fluorescence detection be able to accommodate at least four automated Filters (computer-controlled), allow an easy access, installation and exchange of Filters without special tools or intervention of the company to obtain optimal imaging conditions. Technical specifications Supply Laser scanner imager 3
The laser and filters provided within the instrument shall be compatible with and allow the detection of proteins/dna with the following dyes: Applications Dyes Fluorophores Alexa Fluor: (488, 532, 546, 635, 633, 555, 700, 790), Cy2, Cy3, Cy5, FAM, FITC, HEX, R6G, TAMRA, Texas red; IRDye680, IRDye700, IRDye800, GFP; Multiplexing DIGE (Cy2, Cy3, Cy5, Cy7); G- Dye (100, 200, 300, 400); Dylight (488, 550, 650); ProQ Diamond, ProQ Emerald, Sypro Ruby, ECL Plex Cy2, Cy3 Protein stains Deep Purple, Flamingo, Nile Red, Sypro orange, Sypro Red, Sypro Ruby, Lumitein, Krypton DNA stains Ethidium Bromide, Sybr Gold, Sybr green I and II Chemifluorescence AttoPhos, ECL plus Radioisotopes screen (such as K screen) Colorimetric Coomassie Blue, Copper stain, Silver stain High versatility: the laser scanner shall be able to perform: Fluorescence, Multifluorescence, 2D DIGE (2-D Fluorescence Difference Gel Electrophoresis), 2D no DIGE, Near IR fluorescence imaging, Chemifluorescence, Radioisotope-labeled imaging, Filmless autoradiography, Array imaging, Visible imaging (Coomassie, silver stain...), Phosphor imaging, for gels, blots, arrays, microplates Specific applications: the system shall be adapted to perform a wide range of imaging modes and complex analysis applications such as: Protein identification, characterisation Multi-Protein quantitation (multiple proteins in a same gel/blot) Purity assessement analysis Post-translational modifications (glycosylation, phosphorylation, isoforms ) identification and measurement Screening Multiplexing Technical specifications Supply Laser scanner imager 4
Comparative analyses to address processing and formulation effects (stability, denaturation, modifications ) Differential protein expression analyses The laser based scanner/imager shall be able to acquire data with a confocal scanning to improve the sensitivity and decrease the background for the detection of really low abundant proteins (impurities). High sensitivity and imaging quality to: Allow precise quantitation of proteins, nucleic acids, and other biomolecules in gels, blots, microplates. Have low limits of detection to detect low quantities of proteins: typically o 0.1-2 ng protein (post-fluorescence stain), o 15-50 pg protein (prelabelled fluorescence stain in 1D gel), o < 10 ng protein (visible post stain). Measure subtle changes (< 10 %) in protein expression among low amounts of biomolecules in complex mixtures. For very sensitive detection of low abundant proteins, the system shall be based on a confocal scanning mode. High resolution: Shall be able to go as low as 10 µm. Higher resolutions (25-1000 µm pixel resolution) will be used to prescan the gel/blot to determine the settings to adapt (photomultiplier) or when needing less resolution. Large dynamic range: Shall have a linear signal response over five orders of magnitude for the different imaging modes in gels, blots, tissue sections, and arrays enabling the measurement of low and high abundant proteins in a matrix in one scan as well as the accurate quantitation of subtle changes in protein expression. The system shall have the possibility to simultaneously scan two DIGE gels, each measuring up to 20 x 25 cm to improve comparisons among gels, blots The signal uniformity shall be equal or better than 5% over the entire scan area. Software Full software package(s): Full licence versions for instrument control, data inspection, data analysis, calculation and presentation. Instrument control Full control of the instrument (scan imager) and instrument accessories. Technical specifications Supply Laser scanner imager 5
Full access to all instrument functions: definition of parameters, operations and data acquisition parameters and tests protocols. User-friendly, powerful and flexible to address complex analyses. Full access to raw data: (raw data acquired without any transformation or correction should always be accessible for traceability. Perform data acquisition, recording, data processing, experimental design and statistical analysis. Automation to obtain consistent and objective analysis results, the software packages: Shall possess high levels of (customizable) automation but also allow full manual control for detection and quantitation. Shall have the ability to perform the full analysis in an automatic way of many different types of samples (1-D electrophoresis gels, Dot blots, colony counting; microplates, and basic arrays; user-defined gel analysis) including multiplexed images (multichannel), large volumes of 2-D gel data. Image visualization: the software packages shall Include flexible, extensive and adaptable display/visualisation and process data tools. Be able to handle data acquired in different analyses modes (multiplex, fluorescence, colorimetry, chemifluorescence ), gel types (1D, 2D), and membranes (western blot ) Give the possibility to open several images simultaneously, to overlay multi-channel images (at least three samples in each gel) for match editing and spot editing (gels or blots ). Data processing, evaluation and calculation The software shall: Have powerful analysis functionalities allowing the process of raw data. Possess comprehensive and extended editing functions to transform the raw images prior to and at each stage of the analysis (functions: crop, rotate, filter images, lane creation, background substraction, band detection, molecular weight calibration, quantity calibration, normalization ). Carry out extended and accurate analysis of acquired data from single-plex or Multiplex data (single, multicolor stains files), 2-D gel data (both 2-D DIGE and non-dige). Perform effective spot detection, accurate spot quantitation, and robust gel matching with gel overlay for delivery of accurate results. Technical specifications Supply Laser scanner imager 6
Be able to do simultaneous detection of multiple target proteins on the same gel/blot of both highand low-abundant proteins with high linearity across a dynamic range. Perform Differential In-gel Analysis including codetection, background substraction, normalization, and quantitation of spots in images from 2-D gel (2-D DIGE gel or not) and blot experiments. Perform Batch processes analyses including automated detection, quantitation, matching of multiple 2D DIGE gels and/or blots, comparison between gels with statistical analysis on the protein abundance changes and accurate quantitation of differences in protein expression. Possess warping functions improving matching accuracy and evaluation of matching results. Post run data manipulation: Calibration and normalization Ability to eliminate gel-to-gel variation in 2-D gel electrophoresis for gels as well as gel matching comparisons to reveal real biological variation by: Performing calibrations with markers and internal standards to obtain highly accurate, reproducible quantitation of gel spot (proteins), and accurate comparison of abundance of spots across gels. Performing normalization of the results (abundance values) with internal standard and/or spiked proteins to samples when comparing heterogeneous sample groups (eg: when following a purity analysis process: where proteins abundance between samples differs or proteins are poorly represented). Statistical analysis: the software packages shall Be powerful to handle big data sets and spot maps (up to 1000). Perform advanced statistical analysis for characterization and classification of samples based on protein expression data Perform full statistical and comparative analysis of 2-D DIGE data with multivariate statistical analysis (allowing calculation, interpretation and reports) for easy and fast data mining of 2-D DIGE (biomarker discovery, patterns in expression data), via matching of multiple 2-D DIGE gels to determine protein abundance changes and spots real differences with statistical confidence. o Possibility to combine analyses of different datasets for the biological interpretation of results. Technical specifications Supply Laser scanner imager 7
o Possibility to perform Principal component analysis (PCA) of expression to identify the dominant patterns in the data, such as groups, outliers, trends. o Possibility to perform profile Pattern analysis: to obtain protein expression patterns (e.g., proteins and spot maps with similar expression profiles). o Possibility to perform discriminant analysis: to discriminate proteins between different samples (biological markers), with the possibility to create classifiers, to assign samples to known classes depending on expression profiles. Possibility to detect and quantitate minute protein expression variations across gels or between different gel populations and to reveal true differences in protein abundance between/among samples. Differences in protein levels as little as 10% shall be possible. Results reporting and presentations: the software packages shall Possess a versatile search engine for formulating complex queries without difficulty, and answering biological questions. Provide output of the images exclusively in the form of square root encoded 16-bit TIFF files and optionally as TIFF files. The square root encoded 16-bit TIFF file is required to be able to resolve spots at really low signal levels (impurity levels which need to be detected and estimated). Give the possibility to create pick lists of specific proteins. Possess extended display and Reporting features (Overlay printing in colours and patterns, annotation capabilities to link gel objects). Allow automatic/ customize report creation with full user control including images, lane reports, and gel information for publication. Allow the creation of publication-quality overlay images. Allow Importing/exporting data: Possible import data and image viewer functionality. Possible export of data, high-resolution images, and graphics to software packages: spread sheet, ASCII and/or Microsoft office for their presentation. Allow saving and reloading entire experiments in XML format, exporting spot data for further downstream analysis. Technical specifications Supply Laser scanner imager 8
Compatibility: The software packages shall be compatible with Windows 7 (32-bit and 64-bit). Fully detailed technical requirements of the computer needed to control the system and to perform the analysis shall be provided. Accessories The system shall be delivered with: A second dimension electrophoresis system able to handle precast 24 cm (10-12% or gradient) gels including its power supply Trays/ Frames to accommodate: Agarose and polyacrylamide gels, membranes (nitrocellulose, PVDF) Phosphor screen Microtiter plate, cell culture plates, tissue slides Glass plates (Low fluorescence) with 2D DIGE or agarose and polyacrylamide gels within glass plates. The frames/trays shall be easily removable from the system to be cleaned. Filters: at least the corresponding filters with narrow bandwidth (< 25 nm) for 2D DIGE application (CyDyes; G-Dyes), Fluorescent post-stain (sypro ruby, Krypton, Lumitein, Oriole, Flamingo, Deep purple, FITC, ProQ Diamond, ProQ Emerald ) IP (Phosphorimaging), Near infra red application (IRDye, Cy7). Shall include a printed version of User and software Manuals as well as a pdf version provided on a USB or CD. The electrical connections of the instrument, accessories and connections to the computer shall be adapted to Belgium (230V, 50 Hz; type C/Eplugs, E sockets) 4.2 Validation, Installation, training, warranty and maintenance service 4.2.1 Validation Installation performed including the IQ/OQ/PQ requirement according to ISO 17025:2005 or equivalent. 4.2.2 Installation and training On-site installation and full training for at least 2.5 days for 2 people. The price and description of the training has to be included in the offer. The training has to cover basic functioning, shall address the different measurement technologies, the familiarisation with the software(s), specific applications as well as Technical specifications Supply Laser scanner imager 9
troubleshooting. The training sessions have to be arranged by mutual agreement between the trainer and the trainees. The training has to be given in the English language. 4.2.3 Delivery Supply, installation, validation and training shall be done within 3 months from the date of entry into force of the contract. 4.2.4 After sales service A helpdesk service must be available within 24 h (by telephone and e-mail in English). Time for response on site <72h. 4.2.5 Application support Specialist application support shall be included. 4.2.6 Warranty and Maintenance Full warranty must be foreseen for a period of two years after delivery and acceptance of the requested equipment by the signature of the certificate of conformity by the Commission. This full warranty shall include a full maintenance: One yearly preventive maintenance Corrective maintenance(s) if necessary Spare parts covering the warranty period. The supplier must provide the cost of one year maintenance contract (annually renewable up to a maximum of three years) on the basis of one preventive and if necessary corrective maintenance visits per year. This preventive maintenance shall also include an upgrade or update of the installed software if needed. These yearly maintenance services are to be provided after the two years' warranty period and only if released by JRC-IRMM. 5. Acceptance of this call for tender The tenderer assures that he has proved the completeness of the content of this tender and that it is neither incomplete nor ambiguous. By signature, the tenderer admits that he acknowledges this tender as legally binding in case the Contract is awarded. Place... Date... The tenderer (Stamp and signature)... Technical specifications Supply Laser scanner imager 10