ADVANCED AUTOMATED SOLUTIONSFOR

STRUCTURE ELUCIDATION PROBLEMSUSING

THE MASSPEC ALGORITHM AND

TANDEM MASS SPECTRAL DATA

Marshall M. Siegel, Gary Walker

MS Mass Spec Consultants39-24 Grant St.

Fair Lawn, NJ 07410201 791 1627

siegelmarshall@hotmail.com

CPSA 2012, October 3, 2012, Langhorne, PA

MASSPEC: Software for correlating chemical structures with mass spectra

1. Converts a chemical structure [or library of chemical structures (Batch Mode)]to superatom structures Postulate: Superatom substructures are NOT expected to fragment in the mass spectrometer.

2. Correlates superatom substructure masses with mass spectral fragment ion data3. Scores the fit of the fragment ion data to the superatom structures for obtaining the best

fitting chemical structure.

Applications1. Small Molecules (Natural Products, Pharmaceuticals, Metabolites, Polysaccharides, Peptides)

a. Known Structures: assign substructure to fragment ion massesb. Unknown Structures: Compare library of candidates to mass spectrum to find

highest scoring structure2. Metabolomics

a. Known pharmaceutical (Bonded Superatom), primary metabolite (Floating SA)b. Unknown metabolite: Compare a library of possible precursor candidate

structures to metabolite mass spectrum to find the highest scoring precursor structure

3. Proteomicsa. Determine sites of post-translational modificationsb. Analysis of peptide mixtures.

MASSPEC Characterization of Synthetic Heparin (Arixtra) with 10 Negative Charges

Bonded Superatoms Floating Superatoms

1. ESI CID MS/MS of [ M10- Na7+ ] 3-

2. 8 Sulfates, 2 Carboxylates, 6 Sugar OH’s (H2O)3. All ions converted to single negative charge4. All solutions have z = 1-; All excized ions are excluded.5. All glycosidic O’s expressed as H2O to account for H rearrangements.

1-

1-

1-1-1-1-

1-

1-1-

1-

Metabolomics with MASSPEC –Scoring of Structures with Mass Spectrum

MS/MS Spectrumof Metabolite

Compare Spectrumwith List of

Superatom Structures

Obtain Matching Scorefor Each Natural Product

O

N

O

O

N

O

O

O

N O

O

N

N

NO

N

O O

O

N

O

O

O

N O

O

N

N

N

NorcardamineMetabolite

561.3614 ; 100443.2506 ; 28401.2399 ; 24361.2448 ; 20319.2342 ; 60283.1289 ; 4243.1344 ; 100201.1237 ; 63183.1132 ; 1284.0804 ; 8

NorcardamineMetabolite

Norcardamine Norcardamine Superatoms

MASSPEC Exact Mass Analysis for an Unknown (Data Courtesy of Cerno Bioscience)

EI Mass Spectrum 20 Masses Analyzed

Three Classes of Proposed Elementals for the Unknown Parent Ions (D=Theory-Exp)

I: C6H12N2O4S2, D = -43.8 mmuII: C4H8N4O4S2, D = -18.7 mmu

III: C7H12O5S2, D = +32.0 mmu

m/z ; Intensity239.980 ; 17252.1211.990 ; 32430.4195.970 ; 495.7184.945 ; 439.7165.910 ; 36.3161.995 ; 80.8149.035 ; 2594.5146.965 ; 740.9141.835 ; 42.7131.980 ; 9673.2121.000 ; 10559.8118.975 ; 1485.9104.980 ; 738.993.955 ; 3801.591.975 ; 13936.975.955 ; 5682.664.930 ; 2524.858.000 ; 2083.947.965 ; 2633.442.025 ; 83276.3

Unknown Structure with MASSPEC – Scoring of Structures with Mass Spectrum

74 Structures (Mol Files)Converted Automaticallyto Superatom Structures

Highest Score BestStructural Fit

Modify Best Structure:ProduceHigher Scoring

Superatom Structure

MS000019

MS000027

MS000018

MASSPEC: A computer program for mass spectrometry that utilizes Combinatorics and Graph Theory Methods

to exhaustively compute 1. Superatom substructures of chemical structures, 2. Correlates substructure masses with mass spectral

fragment ion data3. Scores fragment ions based on mass accuracy (D) and

total number of disrupted bonds (N):

Score a {1/D and 1/N}

MASSPEC mimics an approach taken by applied mass spectrometrists to elucidate chemical structures.