Mass Spectral Evaluation Support Services

The purpose of this amendment is to provide answers to all questions received in response to the solicitation and extend the quotation submission due date to 5:00 PM ET on Wednesday, 4/26/2017. All other terms and conditions of the original posting remain unchanged. 1. Task 1: Would the government provide an example of a Work Package? Answer: Example work packages are available at the following web pages: http://chemdata.nist.gov/InChI/EI/work_ei.zip http://chemdata.nist.gov/InChI/EI/work_proteome.zip 2. Task 1: Quality control is not specified in details. It can be different for different types of samples it. For example, in case of synthetic peptides, the quality of the sample is related to a presence (contamination) with synthetic byproducts in addition to a synthesized sequence. In case of "human derived peptides" the quality control for MS1 spectra and for tandem (MS2) spectra is determined by significantly different metrics. Question: should the Contractor define what could be the metrics for quality of the spectra originated from different types of peptides, for MS1 or MS2 spectra, etc, or NIST has a particular guidance? Answer: The vendor should provide their own criteria for quality in their quotation. 3. Task 1: Score thresholds- Contractors should understand that these terms are statistical. If NIST provides N spectra of the same LC-MS runs (replicate), the quality thresholds should be specified differently for each N. Is this accurate? Answer: The vendor should provide their own proposed score thresholds and justifications in their quotation. 4. Task 1: NIST has only MSGF+, Mascot, Sequest and PEAKS , NIST PepSearch . Should contractors expect to use only those search programs or only select programs based on the individual work package? Will any addition search programs be made available to contractors? Answer: NIST will provide PepSearch, and MSGF+ is freely available. No additional programs will be provided by NIST, but the vendor may propose to use other software, including software that is not explicitly listed, if available to the vendor. 5. Task 1: "Each work package may contain a set of runs from 2D studies (typically 24 files) or from a set of closely related samples (typically 12 files). Each work package will require an equivalent level of effort". Will the government please elaborate with examples and details for 2D studies, peak position and its intensity, or the LC retention time is also a parameter. Answer: The use of retention time is not essential. The example work packages provided above include a 2D example. 6. Task 1: "It is anticipated that each work package will require 60 hours of work for completion". Does this mean that NIST will limit the total billable house for task 1 to 60 hours of work on each package x 6 packages = 360 hours? Answer: The number of hours anticipated is provided for informational purposes only to facilitate submission of a Firm Fixed Price quotation. The vendor should price Tasks 1 and 2 as a Firm Fixed Price. 7. Task 1: Will the government provide examples for "...TPOC and COR in an electronic format suitable for computer processing"? Answer: Excel spreadsheet or equivalent. 8. Task 2: A. "...spectral quality control services of tandem and electron ionization mass spectra needed prior to inclusion in the NIST/EPA/NIH Mass Spectral and NIST Tandem libraries, which will involve the processing of mass spectral data files delivered to the contractor by the TPOC ("work packages"). What are the exact parameters of spectral quality expected for the contractor to deliver for each work package? Answer: This requires that the spectra originate from the stated compound and have sufficient peak information to establish that.