Ion fragmentation of small molecules in mass spectrometry. Mass spectrometry is a destructive method used to measure molecular weight and provide. That is covered in three other pages which you can get at via the mass spectrometry menu. Similarly, in a mass spectrometer the generated ions are separated in the mass analyzer, digitized and detected by an ion detector. Mass spectrometry can be used to determine the accurate molecular mass and structural features of an organic compound. In the prism, light is separated into its component wavelengths which are then detected with an optical receptor, such as visualization. These reactions are well documented over the decades and fragmentation pattern is useful to.
Feb 10, 20 in mass spectrometry no characteristic selective absorption of radiation is involved as in the case of the other three methods, secondly, in the mass spectrometry, the compound undergoes irriversible chemical changes unlike in the others, where the changes are reversible physical changes. Mass spectrometry the mass spectrometer bombards the sample with electrons this knocks one electron off the molecule and forms a cation with the same mass as the molecular mass. Bacterial identification by mass spectrometry mark fisher, ph. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low. Order of radicalcarbocation loss tertiary secondary primary methyl hydrogen loss of longest is preferred 4. Mass spectrometry fragmentation patterns last updated. Fragment ion stability takes precedence over radical 5. Fragmentation mechanisms in mass spectrometry journal of. By convention, m by convention, m is the numerical value for the mass of the ion and z is the numerical value for the charge of the ion. Pdf the fragmentation of unsubstituted and substituted 1phenylselanylazulenes, as well as of the corresponding selenoxides and. We have developed an experimentally uncomplicated microscale secondsemester organic lab exercise that illustrates the use of isotopic labeling, in this case deuteration, to help confirm and interpret mass spectral fragmentation patterns in butyl acetate.
Application of fragmentation mechanisms for the assignment of some of the higher mz fragment peaks in appearing in ei mass spectra are shown in figures 11, 12, and for a ketone, and amine and an ester, respectively. Product ions are characterized with the second mass analyzer. The associated acronym, lcms liquid chromatography mass spectrometry covers a. Synthesis and mass spectrometry studies of branched oxime. The chapter includes an introduction to the main ionisation techniques in mass spectrometry and the way the resulting fragments can be analysed. Computational mass spectrometry for smallmolecule fragmentation. Protein sequencing and identification with mass spectrometry. Mass spectroscopy definition of mass spectroscopy by the. In the stick diagram showing the mass spectrum of pentane, the line produced by the heaviest ion passing through the machine at mz 72 is due to the molecular ion. This section will ignore the information you can get from the molecular ion or ions. Some helpful reminders for mass spectrometry and compound. Pdf the fragmentation of unsubstituted and substituted 1phenylselanyl azulenes, as well as of the corresponding selenoxides and.
Which of the following compounds will give a molecular ion having mz an odd number. Mass spectroscopy minnesota state university moorhead. Illustration of fragment ions formed from the backbone cleavage of protonated peptides. The book emphasizes the use of this important analytical technique in many different. By convention, m is the numerical value for the mass of the ion and z is the numerical value for the charge of the ion. Searching spectral libraries, fragmentation spectrum prediction, fragmentation trees.
Organic lecture series 3 mass spectrometry ms organic lecture series 4 a mass spectrometer a mass spectrometer is designed to do three things convert neutral atoms or molecules into a beam of positive or negative ions separate the ions on the basis of their masstocharge mz ratio measure the relative abundance of each ion. The positive fragments which are produced cations and radical cations are accelerated in a vacuum through a magnetic field and are sorted on the basis of mass tocharge ratio. Get private tutoring from anywhere in the world, via your computer, f. Mass spectrometry is a wideranging analytical technique, which involves the production and subsequent separation and identification of charged species.
Pdf computational mass spectrometry for smallmolecule. Tandem mass spectrum tandem mass spectrometry msms. This website offers problems and solutions corresponding to each chapter of mass spectrometry a textbook, 3rd edition. Fra gment ions retaining the positive charge on the amino terminus are termed a, b, or ctype ions. Computational analysis of fragmentation data requires novel strategies. Tandem mass spectrometry msms is a key technique for protein or peptide sequencing and ptm analysis. In mass spectrometry, a substance is bombarded with an electron beam having sufficient energy to fragment the molecule. It is sometimes found that a molecule containing a ketogroup undergoes. Comparison between sourceinduced dissociation and collision. We examine how fragmentation can occur repeatedly with a given substance, and how it helps us to breakdown the structure. Etd and ecd mass spectrometry fragmentation for the characterization of protei n post translational modifications 163 fig. A number of tables can be downloaded through this page. Mass spec fragmentation an extremely useful result of ei ionization in particular is a phenomenon known as fragmentation.
Electronimpact ionization sample inlet 107 108 torr rh electron beam 70 ev 6700 kjmol. Pdf the diagnostic value of the ortho effect for unknown identification by mass spectrometry is well known. Indeed, mass spectrometry appears to be regarded as a mysterious method, just good enough to. In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The leading scientist in this field was fred mclafferty who together with frantisek turecek has written a very. Collisioninduceddissociation results in fragmentation. Mass spectrometry in structural and stereochemical problemscxcviii. Some helpful reminders for mass spectrometry and compound identification degrees of unsaturation in your text, section 3. A mass spectrum is obtained showing a plot of the relative abundance of the ions detected against the mass tocharge ratio.
Pdf meta elimination, a diagnostic fragmentation in mass. Electrospray mass spectrometry and fragmentation of nlinked. The fragmentation pattern is characterized by peaks separated by 14 mass units a ch 2 group. Mass spectroscopy mass spectrometry is the study of systems generating the formation of gaseous ions, with or without fragmentation. The two most important peaks in any mass spectrum are the base peak and the molecular ion peak. Mass spectrometry dont call it spectroscopy absorption of electromagnetic radiation electron impact mass spectrometry 70 ev 1614 kcalmol contrast with energy from ir 110 kcalmol or nmr 0. Professor davis uses pentane to demonstrate the electron impact ionization process and fragmentation patterns in mass spectrometry of alkanes. Evaluation of the mass spectrometric fragmentation of codeine.
Protein digestion for mass spectrometry thermo fisher. The fragments of a molecule cause a unique pattern in the mass spectrum. The leading scientist in this field was fred mclafferty who together with frantisek turecek has written a very famous text book. It is the mz that is furthest intensities to the right. Mass spectrometry ms is an analytical chemistry technique that helps identify the amount and type of chemicals present in a sample by measuring the mass tocharge ratio and abundance of gasphase ions. Fragmentation takes place producing parent ion and ion fragments. When students ask what books to read on mass spectrometry, there are various excellent monographs, but the ideal textbook still seemed to be missing at least in my opinion. Among these methods, mass spectrometry represents the most advanced technique because of its high sensitivity and specificity and the possibility to determine the desired substance in not highly purified samples by using lcmsms. The other lines in the mass spectrum are more difficult to explain. Mass spectrometry is a gas phase technique the sample must be vaporized. The ionized molecule often fragments into smaller ionsradicals. Among several formats, trapped ion mobility spectrometry tims is attractive due. This allows adding ion mobility as a third dimension of separation. It is used for determining masses of particles, for determining the elemental composition of a sample or molecule.
Fast atom bombardment fab matrixassisted laser beam desorption ionization maldi chemical ionization ci and many others. The book emphasizes the use of this important analytical technique in many different fields. Ion fragmentation of small molecules in mass spectrometry uab. For a series of benzenesulfonamides of anilines that bear various substituents, we found that the sulfonamides are preferentially protonated at the nitrogen. The guide arose from discussions held at the vam mass spectrometry working group and was. The radical cation that is produced when an electron is knocked out of a neutral closedshell molecule in eims initially possesses a lot of energy. Mass spectroscopy mass spectroscopy is a technique causing the formation of the gaseous ions with or without fragmentation. Nov 01, 2016 what do you get when you blow molecules up. Mar 10, 2017 mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. With contributions from noted experts from europe and north america, mass spectrometry instrumentation, interpretation, and applications serves as a forum to introduce students to the whole world of mass spectrometry and to the many different perspectives that each scientific field brings to its use. Jan 30, 2014 in this video, we look at the idea of fragmentation in mass spectrometry.
Mass spectrometry ms is recently playing an important role in studying biological samples. Peptide analyses by mass spectrometry arthur moseley arthur. An increase of these may make it difficult to for the electric field to produce the desired charged aerosol. General mass table elemental mass values, amino acid residues and immonium ions. Fragmentation patterns in mass spectra chemistry libretexts. In the past 30 years, mass spectrometry ms has undergone a spectacular devel opment, in terms of. Specific labeling with stable isotopes 2 h, c, 15 n and 18 o is also of importance in mass spectrometry for. In this method, gasphase peptideprotein cations are internally heated by multiple collisions with rare gas atoms. A mass spectrum plural spectra is a plot of the ion signal as a function of the mass tocharge ratio. Size effect on fragmentation in tandem mass spectrometry article in analytical chemistry 826. Etd and ecd mass spectrometry fragmentation for the.
Compatible with a broad range of compounds fg pg sensitivity qualitative information mw up to 100,000 daltons or more with 0. Following are examples of compounds listed by functional group, which demonstrate patterns which can be seen in mass spectra of compounds ionized by electron impact ionization. Fragments lost as neutral molecules in positive ionization mode, a trace of formic acid is often added to. Mass spectrometry and free radicals really radical cations when an organic molecule is ionized in an ms instrument, especially by ei, it generates a radical cation. A relative intensities of the molecular ion and fragments of benzoic acid in electron impact ionization at various electron energies barker. Components of tandem mass spectrometer ms1 collision cell ms2 31aug14 solairajan 102 103.
Fragmentation mechanisms in electron impact mass spectrometry. Formation of small micron sized droplets is not a problem if flow rate, surface tension are low. Estimating the efficiency of phosphopeptide identification by. When nonmass spectrometrists are talking about mass spectrometry it rather often sounds as if they were telling a story out of poes tales of mystery and imagination. These reactions are well documented over the decades and fragmentation pattern is useful to determine the molar weight and structural information. Chapter 2 fragmentation and interpretation of spectra 2. Furthermore, from the perspective of providing crosssectional area for a target, the molecule is composed of mostly free. From the time of the second edition published in 2001 until now, much progress has. Dec 22, 2010 mass spectrometry mass spectrometer is similar to a prism. Ms ms mclafferty, 1978, tandem in space or time precursor ionparent ion. Ion formed by addition or the removal of one or several electrons to or from the sample moleculeselectron impact eims. Introduction mass spectrometry ms is an analytical technique that measures the mass tocharge particles. First, the fundamental notions of mass spectrometry are explained, so that the reader can easily cover this chapter graphs, main pick, molecular ion, illogical pick, nitrogen rule, etc.
Therefore, mass spectroscopy allows quantitation of atoms or molecules and provides structural information by the identification of distinctive fragmentation. Introduction to ionization and fragmentation in mass. The mass to charge ratio mz is used to describe ions observed in mass spectrometry. Algorithms and tools for analysis and management of mass. Five fundamental strategies for computational analysis of fragmentation data. The mechanism of fragmentation of cannabinoids to fragments me 314, 299, 271, 258, 246, 243, and 231 is given. Also find out how fragmentation of molecules can be used to identify a substance and why you have to be positive about. The atomic charges of atoms are found to be good predictors of the fragmentation pathways. Mass spectrometry fragmentation patterns chemistry. Lecture notes in eimass spectrometry by torben lund. Pdf a fragmentation study of dihydroquercetin using. The mclafferty rearrangement is a reaction observed in mass spectrometry during the fragmentation or dissociation of organic molecules. For example, lines with mz values 1 or 2 less than one of the easy lines are often due to loss of one or more hydrogen atoms during the fragmentation process.
Mass spectrometry for proteomics pubmed central pmc. Department of organic chemistry, imm, radboud university nijmegen. M stands for the mass of the molecule that is being tested. It consists in generating a signal spectrum of values mz, intensity related to the presence of a biomolecule with a certain mass tocharge ratio mz, and abundance intensity in the original sample. Collisioninduced dissociation cid has been the most widely used msms technique in proteomics research. Size effect on fragmentation in tandem mass spectrometry. In order to determine which of the derivatives gave the most intense signals when prepared as described above, saturating concentrations from millipore ziptips of glcnac 2 man 5 i, derivatized with each of the amines, were mixed and examined by microflow electrospray from methanol. The mass spectrometry of a number of 6substituted coumarins was studied in the context of correlating fragmentation pathways and electronic charges of atoms performed by am 1 semiempirical method.
Try writing the mechanisms with fish hook arrows using figures 8 and 9 as a guide. The process typically involves either chemical or electron impact ionization of the analyte. Fragmentation of oxime and silyl oxime ether oddelectron positive ions by the mclafferty rearrangement. The decision to perform in solution or in gel digestion is generally determined by the sample amount andor its complexity. Ionattachment mass spectrometry iams is a form of mass spectrometry that uses a soft form of ionization similar to chemical ionization in which a cation is attached to the analyte molecule in a reactive collision. A mass spectrum plural spectra is a plot of the ion signal as a function of the masstocharge ratio.
A mass spectrometric method using electrospray ionization with triple quadrupole and quadrupole timeofflight hybrid qtof mass spectrometry has been applied to the structural characterization of dihydroflavonols. Performance liquid chromatography hplc, with the detection power of mass spectrometry. When working with mass spectrometry, particularly msms spectra, a number of tables are essential in order to understand these. The tallest line in the stick diagram in this case at mz 43 is called the base peak. Isotopic percentage and nominal mass calculation are also. In solution digestion is recommended for small sample volumes with low to moderate complexity and is more amenable to highthroughput sample. A plot of relative abundance of ions vs mz of all charged particles is the mass spectrum.