Limits...
Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry.

Kind T, Fiehn O - BMC Bioinformatics (2007)

Bottom Line: Only 0.6% of these compounds did not pass all rules.Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions.Corresponding software and supplemental data are available for downloads from the authors' website.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of California Davis, Genome Center, Davis, CA 95616, USA. tkind@ucdavis.edu <tkind@ucdavis.edu>

ABSTRACT

Background: Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas.

Results: An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80-99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries.

Conclusion: The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65-81%. Corresponding software and supplemental data are available for downloads from the authors' website.

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Hydrogen/Carbon ratio (H/C) for 42,000 diverse molecules (containing C, H, N, S, O, P, F, Cl, Br, I, Si) taken from the Wiley mass spectral library.
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Figure 2: Hydrogen/Carbon ratio (H/C) for 42,000 diverse molecules (containing C, H, N, S, O, P, F, Cl, Br, I, Si) taken from the Wiley mass spectral library.

Mentions: Another important constraint for restricting formulas to those that are likely to exist is including element ratios, especially the hydrogen/carbon ratio (see Figure 2). In most cases the hydrogen/carbon ratio does not exceed H/C > 3 with rare exception such as in methylhydrazine (CH6N2). Conversely, the H/C ratio is usually smaller than 2, and should not be less than 0.125 like in the case of tetracyanopyrrole (C8HN5). Figure 2 demonstrates that most typical ratios are found between 2.0 > H/C > 0.5, for example for long chain alkanes (H/C ~ 2) or polycyclic aromatic hydrocarbons (H/C~ 0.5). Frequency distributions were found to be not Gaussian, so limit ranges could not be defined by 3σ or 4σ standard deviations which would cover 99.7% and 99.99%, resp., of all formulas in the data set. Instead, cumulative percentages were used as range limits, given as Table 2 for examining the Wiley spectral database as development set. More than 99.7% of all formulas were included with H/C ratios between 0.2–3.1. Consequently, we call this range the 'common range'. However, a number of chemical classes fall out of this range, and we have hence enabled the user to select 'extended ranges' covering 99.99% of all formulas in this development database (H/C 0.1–6). There are extreme cases for which rules of typical H/C ratios may be overridden, e.g. for the study of fullerenes [41] which have an extremely low hydrogen/carbon ratio such as in C78H12Cl2N2. The implementation of our script enables researchers to exclude certain rules if needed for specific applications.


Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry.

Kind T, Fiehn O - BMC Bioinformatics (2007)

Hydrogen/Carbon ratio (H/C) for 42,000 diverse molecules (containing C, H, N, S, O, P, F, Cl, Br, I, Si) taken from the Wiley mass spectral library.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851972&req=5

Figure 2: Hydrogen/Carbon ratio (H/C) for 42,000 diverse molecules (containing C, H, N, S, O, P, F, Cl, Br, I, Si) taken from the Wiley mass spectral library.
Mentions: Another important constraint for restricting formulas to those that are likely to exist is including element ratios, especially the hydrogen/carbon ratio (see Figure 2). In most cases the hydrogen/carbon ratio does not exceed H/C > 3 with rare exception such as in methylhydrazine (CH6N2). Conversely, the H/C ratio is usually smaller than 2, and should not be less than 0.125 like in the case of tetracyanopyrrole (C8HN5). Figure 2 demonstrates that most typical ratios are found between 2.0 > H/C > 0.5, for example for long chain alkanes (H/C ~ 2) or polycyclic aromatic hydrocarbons (H/C~ 0.5). Frequency distributions were found to be not Gaussian, so limit ranges could not be defined by 3σ or 4σ standard deviations which would cover 99.7% and 99.99%, resp., of all formulas in the data set. Instead, cumulative percentages were used as range limits, given as Table 2 for examining the Wiley spectral database as development set. More than 99.7% of all formulas were included with H/C ratios between 0.2–3.1. Consequently, we call this range the 'common range'. However, a number of chemical classes fall out of this range, and we have hence enabled the user to select 'extended ranges' covering 99.99% of all formulas in this development database (H/C 0.1–6). There are extreme cases for which rules of typical H/C ratios may be overridden, e.g. for the study of fullerenes [41] which have an extremely low hydrogen/carbon ratio such as in C78H12Cl2N2. The implementation of our script enables researchers to exclude certain rules if needed for specific applications.

Bottom Line: Only 0.6% of these compounds did not pass all rules.Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions.Corresponding software and supplemental data are available for downloads from the authors' website.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of California Davis, Genome Center, Davis, CA 95616, USA. tkind@ucdavis.edu <tkind@ucdavis.edu>

ABSTRACT

Background: Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas.

Results: An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80-99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries.

Conclusion: The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65-81%. Corresponding software and supplemental data are available for downloads from the authors' website.

Show MeSH
Related in: MedlinePlus