FAQ:

1) What are the requirements to view this web site properly?
2) What ways are there to search for a compound?
3) What does 'match start of search word' option do?
4) What are all of these unusual names in my search results?
5) What are certificate values?
6) What are quantitative values?
7) What are identification values?
8) Why do some individual peaks on GC data chromatograms appear above or below the chromatogram?
9) Why are some LC-MS peaks labeled as 'unknown'?
10) What software did you use?
11) What libraries did you use?

SRM/D 1950 website navigation tutorial:

Search features
Analyte details
Chromatograms and Spectra



1) What are the requirements to view this web site properly?
Web browsers supporting Java external weblink and JavaScript are required in order to view visualizations of chromatograms and spectra.

2) What ways are there to search for a compound?
Compounds can be searched in three different ways.

3) What does 'Start Of Chemical Name' option do?
Option 'Start Of Chemical Name' can be used only when searching by metabolite name. When selected, the search results are required to match the beginning of the metabolite name. Numbers, indicators of stereochemistry and special characters are always ignored from the beginning of the metabolite name.

match start of search word example 1
Figure 1

match start of search word example 2
Figure 2

4) What are all of these unusual names in my search results?
The site automatically searches across all available synonyms for compounds in the database. If this list is too long, you may want to try the 'match start of search word' option described above.

5) What are certificate values?
The certificate values are those that are found on NIST certificate of analysis for standard reference material 1950. These fall into three categories:
  • Certified - a value for which NIST has the highest confidence in its accuracy in that all known or suspected sources of bias have been investigated or taken into account.
  • Reference - a noncertified value that is the best estimate of the true value based on available data; however, the value does not meet the NIST criteria for certification and is provided with associated uncertainties that may reflect only measurement reproducibility, may not include all sources of uncertainty, or may reflect a lack of sufficient statistical agreement among multiple analytical methods.
  • Information Value - a value that may be of interest to the SRM user, but insufficient information is available to assess the uncertainty associated with the value.

6) What are quantitative values?
These are direct measures of absolute concentration and are typically derived using internal standards.

7) What are identification values?
These are measurements that typically include an analyte identification supported by a measure of relative abundance such as an ion current value or precursor peak area calculation.

8) Why do some individual peaks on GC data chromatograms appear above or below the chromatogram?
Total ion chromatograms (TIC) were generated by Automated Mass Spectral Deconvolution and Identification System (
AMDIS) which is a computer program developed at NIST that extracts spectra for individual components in a GC/MS data file and identifies target compounds by matching these spectra against a reference library. The GC/MS data files which typically contain 3000 to 5000 scans have been compressed in order to decrease the time taken for the graph to display on the web page. To do this a variable compression that simply averages adjacent scans so that the TIC is represented in 1000 to 1400 averaged scans. However, the intensity of the individual peaks has been taken from the processing of the original file by AMDIS. As result the apparent peak of the data may be above or below the displayed TIC. The value of the point is exactly the intensity and location given by the deconvolution with AMDIS. The extracted components are expected to be below the TIC, but the ones that show up above the TIC are the result of a narrow peak being averaged down by the compression.

9) Why are some LC-MS peaks labeled as 'unknown'?
Large chromatographic peaks, in some cases, have been annotated as 'unknown' when no match was found in the NIST MS/MS library.

10) What software did you use?
  • GC-MS: AMDIS was used to deconvolute and identify GC-MS spectra.
  • LC-MS: The NISTMSQC pipeline, which uses ProMS for extracted ion chromatogram analysis and MSPepSearch for MS/MS library searching. The 'g' option was used with MSPepSearch.
For more information on data analysis methods, send questions here (paul.rudnick@nist.gov).

11) What libraries did you use?
For GC-MS, the NIST11 NIST/NIH/EPA Mass Spectral Library was combined with an in-house urine metabolite library to generate a target library (available by request).
For LC-MS, the NIST MS/MS library released with NIST11 was used. This is new NIST data product released in 2011.

Search features:

Compounds can be searched in three different ways.
  • By compound name (full or partial)
  • By InChI key (Example: RZVAJINKPMORJF-UHFFFAOYSA-N)
  • By CAS number (Example: 56-41-7 or 56417)

When searching by compound name search suggestions will appear as search query is being typed in showing the top 10 matches for compounds found in the database that match the search string (fig. 1). figure 1
Figure 1

Option 'Start Of Chemical Name' can be used only when searching by metabolite name. When selected the search results will be matched at the beginning of metabolite name (fig. 2).
figure 2
Figure 2

Otherwise search will match any part of the metabolite name (fig. 3).
figure 3
Figure 3

Analyte details:

Details about an analyte can be obtained by clicking on analyte name in the search results table. Depending on the amount of data available for an analyte up to three tabs may be present for a given compound (fig. 4). figure 4
Figure 4

Structure and Synonyms tab is always present. If the structure of the compound is available it will be displayed in this tab. Links to NIST WebBook and ChemSpider are provided to search for more data about the compound. InChi for the compound can also be downloaded as a text file.

If a derivative compound has been identified by one of the experiments, the structure for that compound is displayed along with a link to view details about the derivative. If more than one derivative compound was identified links to those compounds are provided as well.

Table showing synonym names for the analyte is provided with the main name for the compound highlighted in yellow. The structure being viewed is highlighted - for example in fig. 4 it is the parent structure that is being viewed and in fig. 5 it is the derivative. figure 5
Figure 5

Experimental data tab shows the list of experimental runs available for the compound (fig. 6). Description of the experimental method for each experimental run can be viewed by clicking on the method link. Chromatogram and spectrum of the compound can be viewed by clicking on the run name. These are available for LC-MS and GC-MS runs but not NMR figure 6
Figure 6

Clinical data tab shows clinical values. (fig. 7) figure 7
Figure 7

The fourth tab shows data from the certificate. This tab may show Certified, Reference or Information values (fig. 8). Description of methods and sample preparation for the certificate values can be seen by following available links for each method. figure 8
Figure 8

Chromatograms and Spectra:

Clicking on the run name in the 'Experimental Data' tab will open a new window or tab in the web browser and display chromatogram and a list of analytes for the entire experiment. Clicking on analyte names will display that chemica's spectrum (fig. 9).
figure 9
Figure 9

The graphical display of an experimental run is split into three parts. The table on the left contains all the compounds identified by that run. These compounds are represented on the chromatogram as dots with different colors. Clicking on the compound name in the table or on a dot on chromatogram will bring up the spectrum of the compound and NIST library reference spectrum. Both chromatogram and spectrum viewer have the ability to zoom in and out for a more detailed look at the data. For convenience structure and synonyms tab is added to the spectrum view to display structure of the selected compound in a similar manner as previously described.