A -- Quality Control for Mass Spectra of Metabolites and Peptides

Contracting Office Address: Department of Commerce, National Institute of Standards and Technology (NIST), Acquisition Management Division, 100 Bureau Drive, Building 301, Room B129, Mail Stop 1640, Gaithersburg, MD, 20899-1640, UNITED STATES A. DESCRIPTION: This is a combined synopsis/solicitation for commercial services prepared in accordance with the format in FAR Parts 12 and 13, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a separate written solicitation will not be issued. Solicitation Number NB838050-8-02231rs is issued as a request for quotation. No set-aside is identified for this RFQ. The North American Industry Classification Code (NAICS) is 541712. The National Institute of Standards and Technology has a requirement for technical support services described below. B. EVALUATION OF QUOTE: Best value evaluation factors include the following and are listed in accordance to importance: 1) Approach - The likelihood of effectively meeting the requirements; 2) Past Performance - The relevance and quality of prior performance for similar taskings. Quote must include at least three (3) Past Performance references and valid phone numbers; and 3) Price - The amount, realism and consistency of the evaluated price. The evaluation shall be based on use of the adjectival scheme as follows: Outstanding (O) - Conspicuously striking in eminence; Excellent (E) - Very good of its kind; eminently good, superior or first class; Good (G) - Beneficial and worthwhile; sound and valid; Adequate (A) - Reasonably sufficient and suitable; Marginal (M) - Minimally suitable at the lower limit; Unsatisfactory (U) - Not acceptable, not adequate to carry out. C. APPLICABLE CLAUSES: The solicitation document and incorporated clauses are those in effect through Federal Acquisition Circular Number 2005-14. The provisions and clauses may be downloaded at http://www.acqnet.gov.far. The following provisions and clauses shall apply to this solicitation: FAR 52.204-9, Personal Identity Verification of Contractor Personnel; FAR 52.212-1, Instructions to Offerors - Commercial applies to this acquisition and there is no addendum to this provision; FAR 52,212-2, Evaluation - Commercial Items. The Government shall award a purchase order resulting from this solicitation to the responsible offeror whose offer conforming to the solicitation will be most advantageous to the Government, price and other factors considered. The following factors shall be used to evaluate offers: (i) approach, (ii) past performance, (iii) price. FAR 52.212-3, Offeror Representations and Certifications - Commercial Items, applies to this acquisition and there is no addendum to this provision; FAR 52.212-4, Contract Terms and Conditions - Commercial Items, applies to this acquisition and there is no addendum to this provision; FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items, applies to this acquisition; FAR 52.217-8, Option to Extend Service - The Government may require continued performance of any services within the limits and at the rates specified in the contract. These rates may be adjusted only as a result of revisions to prevailing labor rates provided by the Secretary of Labor. The option provision may be exercised more than once, but the total extension of performance hereunder shall not exceed 6 months. The Contracting Officer may exercise the option by written notice to the Contractor within 10 days. FAR 52.217-9, Option to Extend the Term of the Contract - (a) The Government may extend the term of this contract by written notice to the Contractor within 30 days; provided that the Government gives the Contractor a preliminary written notice of its intent to extend at least 60 days before the contract expires. The preliminary notice does not commit the Government to an extension. (b) If the Government exercises this option, the extended contract shall be considered to include this option clause. (c) The total duration of this contract, including the exercise of any options under this clause, shall not exceed 24 months. FAR 52.227-14, Rights in Data - General. All interested contractors must be actively registered in the Central Contractor Registration (CCR) at the CCR website www.ccr.gov. And other appropriate clauses as need. D. PROPOSAL FORMAT AND DELIVERY: Interested parties are invited to provide an electronic response, with cover letter, to be received no later than 07:00 AM, January 02, 2008, and shall be in either Word or .PDF format. Any other format shall be identified as NON-RESPONSIVE and not considered. E-MAIL TO: raymond.staniewski@nist.gov. Contractors must submit a complete response. Responses that are not substantially complete shall be identified as NON-RESPONSIVE and not considered. Offers of partial performance shall be identified as NON-RESPONSIVE and not considered. Each response shall be formatted to print on 8 1/2-inch x 11-inch paper, in a commercially standard font, not smaller than a font size of 12 point. Submit quotes arranged in three sections as follows: Section I - Approach, which includes identification and qualifications of relevant personnel and technical management approach; Section II - Past Performance, which includes relevant experience which describes at least three (3) relevant projects performed in the last three years and quality of performance and include appoint of contact and phone number; Section III - Price, firm fixed price for the required technical consulting services. Each firm fixed price shall include sufficient data to allow the Government to determine the amount, realism and consistency of the fixed price. Award shall be made to the responsible contractor that offers the best value to the Government. The Government shall not be liable for any costs incurred in response to this request. The Government reserves the right to make a single award, multiple awards, or no award as a result of this RFQ. It is the responsibility of the respondent to confirm NIST's receipt of quote. E. ORIGINAL POINT OF CONTACT: Primary POC: Raymond Staniewski, Purchasing Agent, Phone 301-975-8497, Fax 301-975-3839, E-mail raymond.staniewski@nist.gov Alternate POC: Mario Checchia, Contract Specialist/Contracting Officer, Phone 301-975-8407, Fax 301-975-2541, Email mario.checchia@nist.gov F. PERIOD OF PERFORMANCE: Base Period: 01 MARCH 2008 through 28 FEBRUARY 2009 Option Period I: 01 MARCH 2009 through 28 FEBRUARY 2010 G. PLACE OF PERFORMANCE: *** BULK OF WORK TO BE PERFORMED AT CONTRACTOR'S LOCATION *** National Institute of Standards & Technology 100 Bureau Drive Gaithersburg, Maryland Postal Code: 20899-1640 Country: UNITED STATES PERFORMANCE WORK STATEMENT QUALITY CONTROL FOR MASS SPECTRA OF METABOLITES AND PEPTIDES IT Service, Data Analysis I. BACKGROUND This procurement is being conducted for the U. S. Department of Commerce (DOC), National Institute of Standards and Technology (NIST), Chemical Sciences and Technology Laboratory (CSTL), Physical and Chemical Properties Division (PCPD) in Gaithersburg, Maryland. A collection of about 10,000 reference MS-MS spectra has become a part of the NIST/NIH/EPA mass spectral library (http://www.nist.gov/srd/nist1.htm). The main target for enhancement is metabolites and peptides derived from proteins and synthetically made. This involves: a) Measurement of high quality MS-MS spectra of metabolites and peptides, b) Analysis of spectral data, c) Micro-synthesis of compounds of interest when needed, d) Establishment of computer tools for the quality control for MS-MS spectra, and e) Testing and development of applications of this data and metadata. The specific needs addressed in this order are related to the necessity for obtaining high quality MS-MS spectra of metabolites, peptides and related substances and for developing software tools for analysis of these spectra II. SCOPE OF WORK TASK 1 - The contractor shall experimentally select instrument parameters and establish optimal conditions for obtaining consistent standard positive and negative ion MS-MS spectra for specific classes of compounds on Finnigan LTQ and Micromass Quatro Micro instruments. TASK 2 - The contractor shall measure high quality MS-MS spectra of metabolites and peptides; the spectra obtained in each of the above instruments under positive and negative modes shall be reproducible. The spectra shall be analyzed, and spectrum/structure consistency shall be determined for each case. When unusual behavior under mass spectrometry conditions for a peptide is observed, micro-synthesis of synthetic analogs and modified peptides shall be performed, and the products of micro-synthesis shall be analyzed. TASK 3 - The contractor shall develop software system for determining the quality of MS-MS spectra of metabolites and peptides. The software shall be based on the use of a) known rules for the fragmentation based on the sequence, charge, peptide length and other factors affecting the chemistry and ionization, b) patterns identified by the contractor when analyzing the data from own measurements; c) and algorithms based on more fundamental physical/chemical principles. III. DELIVERABLES AND REPORTS DELIVERABLES FOR TASKS 1-3: 1. Report on the standard methods established for the analysis of peptides and their modified analogs electronically in a text format. 2. Positive and negative ionization MS-MS spectra of metabolites, peptides, and modified peptides electronically in the instrument formats. 3. A detailed report on the methods used for the micro-synthesis of peptides and their modified analogs electronically in a text format. 4. Report on the spectra examination procedures, when unusual behavior of a compound under mass spectrometry conditions being observed, electronically in a text format. Non-data outputs-s: 1. Presentation describing MS-MS spectra of peptides and metabolites at the 56th and 57th Annual ASMS conferences on mass spectrometry (2008, 2009) IV. DELIVERABLE DUE DATES AND/OR PERIOD OF PERFORMANCE Anticipated due dates for each deliverable: Base Period: March 1, 2008 to February 28, 2009 for each deliverable under tasks 1-3. Option Period: March 1, 2009 to February 28, 2010 for each deliverable under tasks 1-3. V. GOVERNMENT-FURNISHED PROPERTY, DATA AND/OR INFORMATION The government will furnish chemicals for mass spectrometry investigation, as well as the peptide synthesizer, Finnigan LTQ and Micromass Quatro Micro instruments. In addition the government will furnish an adequate work space for the contractor, email and internet access, the NIST library access, and any computers necessary to complete the tasks. All work will be done onsite at NIST/Gaithersburg. The HSPD-12 Security Risk Level assigned to this Task order is: Low. VI. PERFORMANCE REQUIREMENT SUMMARY 1. Desired Output - To obtain high quality MS-MS spectra of metabolites and peptides, and to develop software methods for MS-MS spectra analysis. 2. Required Service - a. To establish optimal conditions for obtaining consistent standard positive and negative ion MS-MS spectra for specific classes of compounds on ?Finnigan LTQ? and ?Micromass Quattro Micro? instruments; b. To measure and analyze MS-MS spectra of metabolites and peptides. Perform micro-synthesis when unusual behavior under mass spectrometry conditions for a peptide is observed. c. To develop software system for measuring the quality of MS-MS spectra of metabolites, peptides, and of their modified analogs. 3. Performance Standard - The MS-MS spectra shall be reproducible, and the fragmentation pathways can be explained. The MS-MS prediction software shall include all known fragmentation rules. VII. KEY PERSONNEL REQUIREMENTS The minimum requirements for the work include, but are not limited to, (a) a degree in chemistry or biology for a key personnel, (b) at least one year experience on the solid-state synthesis of peptides and obtaining MS-MS spectra of metabolites, peptides and their modified analogs, and (c) at least a 2 year experience in developing software systems for analyzing MS-MS data; experience with routine MS-MS analysis is not sufficient for this purpose.