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1 Welcome! Mass Spectrometry meets Cheminformatics Tobias Kind and Julie Leary UC Davis Course 4: Mass Spectrometry Tools & Concepts Class website: CHE.

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Presentation on theme: "1 Welcome! Mass Spectrometry meets Cheminformatics Tobias Kind and Julie Leary UC Davis Course 4: Mass Spectrometry Tools & Concepts Class website: CHE."— Presentation transcript:

1 1 Welcome! Mass Spectrometry meets Cheminformatics Tobias Kind and Julie Leary UC Davis Course 4: Mass Spectrometry Tools & Concepts Class website: CHE Spring CRN 16583CRN Slides: PPT is hyperlinked – please change to Slide Show Mode

2 2 Atomic Mass Hexachlorobenzene (C6Cl6) average mass u integer mass u monoisotopic mass u Correct unit is [u] – unified atomic mass unit or [Da] Dalton see SI unitsSI units 1 u = 1 Da = 1/12 th of mass of carbon 12 C = x kg Always (always) check molecular masses obtained from databases or publications. For mass spectrometry the monoisotopic mass is used. InChIKey:CKAPSXZOOQJIBF-UHFFFAOYAVCKAPSXZOOQJIBFUHFFFAOYAV

3 3 MWTWIN Example: Molecular Weight Calculator (Matthew Monroe / PNNL)Molecular Weight CalculatorMatthew Monroe

4 4 Mass Accuracy ppm Linear IonTrap ppm Triple Quad ppm Q-TOF ppm TOF-MS ppm Magnetic Sector ppm Orbitrap ppm FT-ICR-MS Mass AccuracyType (10 ppm in Ultra-Zoom) Instruments must be calibrated to obtain high mass accuracy. In case of FT-ICR-MS mass calibration can be stable over weeks. Post- mass calibration can be performed if calibrant was run with samples. Mass of electron becomes important at around 500 Da. m(e-) = u = mass of electron m(1H) = u = mass of proton

5 5 Resolving Power High resolving power is helpful for separation of species with almost same mass (isobars). High resolving power can not be used to distinguish between structural isomers. Example: C 8 H 10 N 2 O has 100,082,479 isomers. RP = 1700 RP = 48,250 Example Solanine (CID=30185)Solanine

6 6 Isotopic Pattern Generators Elements can be a) monoisotopic (F, Na, P, I) b) polyisotopic (H, C, N, O, S, Cl, Br) Isotopic pattern generators generate the isotopic abundances for a given mass value. Calculation is very time-consuming and based on Fast Fourier algorithms. Example: Molecular Weight Calculator (Matthew Monroe / PNNL)Molecular Weight CalculatorMatthew Monroe

7 7 Isotopic pattern generators Example form Thermo Xcalibur with a very versatile isotopic pattern generator

8 8 Charge states CID: MW = C50H72N13O15P charge state 2 charge state 1

9 9 Different charge states and peak resolutions Example of Phosphorylated Angiotensin isotopic pattern without adduct [M+H] + simulated by Thermo XCaliburPhosphorylated Angiotensin

10 10 Charge state deconvolution z = 2 z = 1 Monoisotopic peaks are shown on the mass spectrum, where z = 1 Example from Decon2Ls Tutorial (PNNL) A Software Tool for Deconvolution of High Resolution Mass Spectra Peaks are detected and charge states are automatically calculated for whole datasets Download Decon2LSDecon2LS Picture sources: PNNL/ Decon2Ls Tutorial

11 11 Adduct formation Adduct formation is observed in ESI, CI and APCI ionization modes (and others). Adduct detection is problematic for small molecules, can be influenced by solvent selection. Adduct detection can be automated if two or more adducts are detected in mass spectrum. Switching polarity (+/-) can be used for confirmation of adduct. Download the Mass Spectral Adduct Calculator

12 12 Molecular Formula Generators Formula generators are used to create molecular formulae from accurate masses. Input requires 1) accurate isotopic mass (with or without adduct) and 2) error in ppm or mDa (milli Dalton) Accurate mass Mass error Example MWTWIN

13 13 The molecular formula space of small molecules calculated by the Seven Golden Rules Source Each molecular formula can expand to billions of structural isomers. Molecular Formula Molecular Isomer

14 14 Frequency distribution of molecular formulas Source: Kind and Fiehn BMC Bioinformatics :234 doi: / doi: /

15 15 Impact of mass accuracy on number of formulas

16 16 Mass accuracy and isotopic pattern Example from: Example: ESI-MS (+) of Solanine on a LTQ Resolving Power: 1700 Mass Accuracy: 46 ppm Isotopic Abundance Error: ±1.46% C45H73NO15 MW = [M+H] +

17 17 Isotopic abundances as orthogonal filter Source: Kind and Fiehn BMC Bioinformatics :234 doi: / doi: /

18 18 Molecular Isomer Generators Isomer generators are used to create all possible structural isomers from a given molecular formula. Deterministic and stochastic (random) generators are in use. Example: MOLGEN DEMO (Bayreuth)MOLGEN DEMO

19 19 The molecular isomer space is unknown Accurate massFormulaNumber Isomersin Beilstein DB CH2O CH6N2O C2H6O C4H2N C5H2O C6H C7H6N2O2100,082, C7H10N466,583, C8H6O36,717, C8H10N2O76,307, C9H10O26,843, C9H14N29,459, C10H2N265,563, C10H14O1,548, C11H2O9,414, C11H1884, C12H634,030,90512 Source: Meringer M: Mathematische Modelle für die kombinatorische Chemie und die molekulare Strukturaufklärung.

20 20 MOLGEN-MS

21 21 Substructure predictions Use computer algorithms (machine learning) for automated interpretation of fragments and corresponding substructures. Algorithms creates present/absent list of substructures. Example from NIST-MS search

22 22 Simulation of mass spectra Why is simulation or prediction of mass spectra important? Molecular isomers (structures) can be generated very fast from molecular formulas Only certain mass spectra can be simulated (MS/MS of peptides, oligosaccharides, lipids) Problematic is abundance determination Problematic are all complex rearrangement reactions (gas phase ion chemistry) Simulation of mass spectra from small molecules is new and important research Experimental spectra Simulated spectra Perform comparison or matching

23 23 Barcode spectrum from Mass Frontier Example: MassFrontier Helpfile

24 24 Peptide Sequence Fragmentation Modelling Example: Taken from Molecular Weight Calculator (Matthew Monroe / PNNL)Molecular Weight CalculatorMatthew Monroe

25 25 Matching experimental vs. theoretical sequence Example: RHPEYAVSVLLR

26 26 The Last Page - What is important to remember: Important performance parameters are accurate mass, resolving power, scan speed and accurate isotopic abundances Even high resolving power MS can not distinguish between structural isomers Accurate Mass Molecular Formula Structural Isomers MS/MS Mass spectra of only some substance classes can be simulated

27 27 Tasks (12 min): (1) Use a Molecular Formula Finder Molecular Weight Calculator Molecular Weight Calculator or any other tool (HR2 in 7 Golden Rules) Calculate how many formulae (elements CHNO) can be calculated for a)m/z at 100 ppm, 10 ppm, 1 pm b)m/z at 100 ppm, 10 ppm, 1 pm (2) Calculate the number of isomers for C12H12 using MOLGEN or CDK (3) Generate the isotopic pattern for Chlorophyll a and Hexachlorobenzene. (4) Download Decon2LS and perform example calculations from tutorialDecon2LS

28 28 Literature (35 min): Debating resolution and mass accuracyDebating resolution and mass accuracy (MP Balogh) Enumerating molecules Enumerating molecules (Faulon) Milestones in fourier transform ion cyclotron resonance mass spectrometry technique development

29 29 Links: Used for research: (right click – open hyperlink) "Sic transit gloria chimica Of general importance for this course:


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