19 F 70 C5H10. Bibliography: Usually the best way to start is by looking for likely breaks in the molecule. 12.3: Mass Spectrometry of Some Common Functional Groups, 12.4: Mass Spectrometry in Biological: Time-of-flight (TOF) Instruments, Organic Chemistry With a Biological Emphasis. Secure .gov websites use HTTPS Have questions or comments? A common fragmentation pattern for larger carbonyl compounds is called the McLafferty rearrangement: The mass spectrum of 2-hexanone shows a 'McLafferty fragment' at m/z = 58, while the propene fragment is not observed because it is a neutral species (remember, only cationic fragments are observed in MS). Subsequent rearrangement on the alcohol side generates m/z=60 and 56 ions. Can you get an alpha cleavage (a break next to a heteroatom like O or N)? Propose a structure, and identify the three species whose m/z values were listed. 2. A common fragmentation pattern for larger carbonyl compounds is called the McLafferty rearrangement: The mass spectrum of 2-hexanone shows a 'McLafferty fragment' at m/z = 58, while the propene fragment is not observed because it is a neutral species (remember, only cationic fragments are observed in MS). Comments regarding the fragmentation patterns are presented in the box to the right of each spectrum. The charge may reside on either fragment, with the larger usually predominating. The mass spectrum of an aldehyde gives prominent peaks at m/z = 59 (12%, highest value of m/z in the spectrum), 58 (85%), and 29 (100%), as well as others. What are the masses of all the components in the following fragmentations? The mass apectra of three different saturated hydrocarbons are displayed below. A) Small molecules (metabolomics, < 2000 Da) can not be sequenced like peptides or proteins … Often the base peak is from an ‘oxonium’ ion. The m/z=81 & 67 ions are smaller homologues of this ion (14 mass units less). It doesn’t have the capacity to make a tertiary cation, either. A lock ( LockA locked padlock Now try the McLafferty rearrangement. Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University), Prof. Steven Farmer (Sonoma State University), Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris). 1. Are there Waters applications for bioanalysis of oligonucleotides in serum? The mass spectrum fits that of propanal. A common fragmentation pattern for larger carbonyl compounds is called the McLafferty rearrangement: The mass spectrum of 2-hexanone shows a 'McLafferty fragment' at m/z = 58, while the propene fragment is not observed because it is a neutral species (remember, only cationic fragments are observed in MS). Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University), Prof. Steven Farmer (Sonoma State University), Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris). Missed the LibreFest? Make certain that you can define, and use in context, the key terms below. The list is suggestive rather than comprehensive, and should be used in conjunction with other sources [1-5]. This cleavage is shown here. In this case both ions are relatively strong (m/z=54 & 56). The main piece of information to remember in answering these types of questions is that each of the structures you draw must be positively charged. ) or https:// means you've safely connected to the .gov website. Draw the fragments responsible for the peaks in the mass spectrum at m/z 71, 58, and 43. Title: What are the common contaminants in my GCMS Contamination is usually identified by excessive background in the mass spectra. After completing this section, you should be able to predict the expected fragmentation for common functional groups, such as alcohols, amines, and carbonyl compounds. Reprinted with permission from NIST. The main piece of information to remember in answering these types of questions is that each of the structures you draw must be positively charged. Propose a structure, and identify the three species whose m/z values were listed. m/z Ions m/z Ions 15 CH363 C5H3 a. The molecule is shown here to make it easy to see which bonds get made and which bonds get broken. Unless otherwise noted, LibreTexts content is licensed by CC BY-NC-SA 3.0. In each example the molecular ion is designated by M •+. The LibreTexts libraries are Powered by MindTouch® and are supported by the Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions Program, and Merlot. Alpha-cleavage gives ions at m/z=57 & 85 Da. If it’s a carbonyl compound, does it have a gamma hydrogen that could be involved in a McLafferty rearrangement? So, alpha cleavage would definitely be a possibility. Odd-electron ions, including the molecular ion, are colored orange when marked. When alcohols are subjected to electron ionization MS, the molecular ion is highly unstable and thus a parent peak is often not detected. Even-electron ions are colored magenta. He received his PhD at the University of Maryland in 2007. The LibreTexts libraries are Powered by MindTouch® and are supported by the Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions Program, and Merlot. We also acknowledge previous National Science Foundation support under grant numbers 1246120, 1525057, and 1413739. Use the Back Arrow to return to a spectroscopy problem Return to Mass Spectrum Home Page. How to Draw Molecular Fragments Based on Mass Spectrum Peaks, Organic Chemistry I For Dummies Cheat Sheet, How to Predict the Equilibrium Direction of an Acid-Base Reaction. Legal. "Automated Data Massaging, Interpretation, and E-Mailing Modules for High Throughput Open Access Mass Spectrometry"; Watch the recordings here on Youtube! Click here for examples of compounds listed by functional group, which demonstrate patterns which can be seen in mass spectra of compounds ionized by electron impact ionization. Legal. When alcohols are subjected to electron ionization MS, the molecular ion is highly unstable and thus a parent peak is often not detected. Ions are sometimes characterized by loss of a specific neutral fragment from the molecular ion. Two are isomeric hexanes and the third is cyclohexane. There are more bars on the graph than just the mass of the sample Much of the utility in electron-ionization MS comes from the fact that the radical cations generated in the electron-bombardment process tend to fragment in predictable ways. "Automated Data Massaging, Interpretation, and E-Mailing Modules for High Throughput Open Access Mass Spectrometry"; Hui Tong, Duncan Bell, Keiko Tabei, and Marshall M. Siegel; Journal of the American Society for Mass Spectrometry; November 1999, Volume 10, Issue 11, pp 1174–1187. The loss of a methyl radical generates the base peak at m/z=95 Da. There are also some common misunderstandings regarding small molecule science and metabolomics which need to be clarified. What are the masses of all the components in the following fragmentations? This, as you might expect, is the result of formation of a methyl cation, in addition to an acyl radical (which is neutral and not detected). b. Common Observed and Predicted Background Ions in ESI Positive Mode Compounds and Species Ions Mass of ions Fragment from acetonitrile CN-26.0036 Formic acid HCOO-44.9982 Acetic acid CH SO-59.0139 Phosphoric acid, and oligonucleotides or phosphopeptides PO 3-78.9591 Sulfuric acid and other sulfated materials SO-79.9574 Methanesulfuric acid CH 3SO-94.9808 Sulfuric acid HSO 4-96.9601 … Two are isomeric hexanes and the third is cyclohexane. Start with alpha cleavage. Draw the fragments responsible for the peaks in the mass spectrum at m/z 71, 58, and 43. The molecule can split on the left of the carbonyl group to make the resonance-stabilized cation that has a molecular weight of 71 amu.

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