Tandem mass spectrometry msms has been widely used for identifying metabolites in many areas. An organic chemists guide to electrospray mass spectrometric. It is commonly used for the identification of organic compounds from electron ionization mass spectrometry. Accurate mass spectra of 37 drugs of abuse and related compounds, including. Fragmentation of ions in ion trap mass spectrometers has traditionally been done using collisionally induced dissociation cid. For the determination of molecular formula by mass spectrometry, it is essential to identify the molecular ion peak as well as its exact mass. Lecture 1 basics of mass spectrometry 1 mass spectrometry. Both lowmassresolving power and highmassresolving power esims were conducted in the negativeion mode on a ltq orbitrap velos and a ltq orbitrap from thermo scientific west palm beach, fl, equipped with the xcalibur operating system. The position of the carbonyl group influences the fragmentation pattern because the molecular ion fragments either side of the carbonyl group. In principle, fragmentation rules can be automatically learned from experimental data using data mining. Even without a ci spectrum of the compound, other rules can assist in. The fragments of a molecule cause a unique pattern in the mass spectrum.
Following the evenelectron rule ee in the electrospray. Pdf general principles of identification by mass spectrometry. 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. The ionized molecule often fragments into smaller ionsradicals. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in substructure identification, while mass spectral trees delineate the dependencies in multistage ms of collisioninduced dissociations. Thompsons later 8 discovery of the electron also used one of the simplest mass spectrometers to. Lipidmatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Using fragmentation trees and mass spectral trees for.
Primary amides show a base peak due to the mclafferty rearrangement. While being quite long, this chapter cannot be comprehensive, and thus, you even might want to look for further reading 1, 2, 3. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. The presence of chlorine or bromine atoms is usually recognizable from isotopic peaks.
Mass spectrometry fragmentation patterns chemistry. Accurate recognition and feature qualify for flavonoid extracts from liangwai gan cao by liquid chromatographyhigh resolution mass spectrometry and computational msms fragmentation. As regards fragmentation behavior, the mass spectra of both approaches 25 were quite similar, and were useful to study the fragmentation of the drugs investigated. Dec 01, 2015 for the love of physics walter lewin may 16, 2011 duration. Mass spectroscopy minnesota state university moorhead. Fragment peaks other than the molecular ion peak is.
Mass spectrometry, third edition provides students with a complete overview of the principles, theories and key applications of modern mass spectrometry. Further development of the chemical modification methods for n. Molecular ion peaks are present, possibly with low intensity. These rules are based on the classic evenelectron rule and cover heteroatoms and multistage fragmentation. That is covered in three other pages which you can get at via the mass spectrometry menu. So, first mass analyzer isolates this masstocharge ratio and sends that on for fragmentation and second, a second mass spec analysis. Since 1994, i have been head of the mass spectrometry laboratory at the chemistry department of heidelberg university where i teach introductory courses and seminars on mass spectrometry. Electrospray ionization mass spectrometry esims sample stock solutions were diluted to 1. Mass spectral fragmentation of trimethylsilylated small.
The mass to charge ratio mz of the ion effects this motion. However, computationally identifying metabolites from msms data is challenging due to the unknown of fragmentation rules, which determine the precedence of chemical bond dissociation. We introduce lipidmatch, an rbased tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. First, the fundamental notions of mass spectrometry are explained, so that the. Fragmentation of organic ions and interpretation of ei. Aug 29, 2017 tandem mass spectrometry msms has been widely used for identifying metabolites in many areas. Unique fragmentation libraries, compared to other open source software, include oxidized. Data system mass detector analyzer vacuum system source inlet region more precisely mass spectrometry determines the mass of a molecule.
Gas chromatography mass spectroscopy introduction gas chromatography mass spectroscopy gcms is one of the socalled hyphenated analytical techniques. Ion fragmentation of small molecules in mass spectrometry. Fragmentation of molecules under mass spectrometry. The number of hits may also be reduced by taking an accurately measured isotope pattern of the ion into consideration. Jun 01, 2015 multistage mass spectrometry msn trees show promise to aid in this regard. The latest edition of a highly successful textbook, mass spectrometry, third edition provides students with a complete overview of the principles, theories and key applications of modern mass spectrometry. Fragmentation tends to occur alpha to the oxygen atom cc bond next to the oxygen. Lecture notes in eimass spectrometry by torben lund. Fragmentation pattern and its rules and interpretation of mass spectroscopy guided by. Mass spectrometry ms is a key technique for qualitative chemical analysis. Although this problem has been tackled by different ways, the lack of computational tools to flexibly represent. Mass spectra is a plot of relative abundance against mass tocharge ratio. This page looks at how fragmentation patterns are formed when organic molecules are fed into a mass spectrometer, and how you can get information from the. Appi is a soft ionization method complementary to esi and apci that uses photo energy to ionize nonpolar small molecules not easily ionized by esi or apci.
The elemental composition and structural information of a molecule can be readily determined by information provided by ms, such as accurate masstocharge ratio mz, isotope abundance and fragmentation patterns. The mechanism for cid, shown in figure 1, does not. For the love of physics walter lewin may 16, 2011 duration. Pdf the fragmentation of unsubstituted and substituted 1phenylselanylazulenes, as well as of the. The guide arose from discussions held at the vam mass spectrometry working group and was. So, this peptide gets fragmented into various pieces as you can see here where again mass to charge ratio over the intensity of each of these different mass charge ratios. Zhurkovich, mass spectrometry analysis of medical samples. The following chapter introduces one of the key disciplines of organic mass spectrometry. Ion formed by addition or the removal of one or several electrons to or from the sample moleculeselectron impact eims. Tandem mass spectrometry is introduced early on and then developed in. All instrumental aspects of mass spectrometry are clearly and concisely described.
A predictive science approach to aid understanding of. Atmospheric pressure photoionization source appi appi is a soft ionization method complementary to esi and apci that uses photo energy to ionize nonpolar small molecules not easily ionized by esi or apci, for example polycyclic aromatic hydrocarbons pahs, expanding the range and classes of compounds that can be analyzed. For mass spectrometry, the manual interpretation of collisioninduced dissociation cid mass spectra is cumbersome and requires expert knowledge, as the fragmentation mechanisms of ions formed from small molecules are not completely understood. Mass spectra is a plot of relative abundance against masstocharge ratio. The structural elucidation of organic compounds in complex biofluids and tissues remains a significant analytical challenge. From the time of the second edition published in 2001 until now, much progress has. In this study, we propose nine rules of hydrogen rearrangement hr during bond cleavages in lowenergy collisioninduced dissociation cid. For the analytical chemist, a mass spectrum is useful for two applications. From 556 tested fragmentation patterns, 228 rules yielded true positive hits within 4 mda mass accuracy. Monoisotopic mass is typically expressed in unified atomic.
General principles of identification by mass spectrometry. Fragmentation of oligosaccharides from sodium adduct. The leading scientist in this field was fred mclafferty who together with frantisek turecek has written a very famous text book. Introduction to ionization and fragmentation in mass spectrometry. Rearrangements are common but usually do not give intense peaks. Fragmentation rules for organic and organometallic compounds under ei d. These fragmentation rules were subsequently validated by specificity and sensitivity assessments using the nist 14 nominal mass library and a new in. Mass spectrometry fragmentation patterns chemistry libretexts. The mass to charge ratio mz is used to describe ions observed in mass spectrometry. Although this problem has been tackled by different ways, the lack of computational tools to flexibly. Instead, mass spectrometry is based upon the motion of a charged particle, called an ion, in an electric or magnetic field. Spectroscopy vs spectrometry spectroscopy latin specere. The metabolomics standards initiative msi categorizes.
As the name implies, it is actually two techniques that are combined to form a single method of analyzing mixtures of chemicals. Computing fragmentation trees from tandem mass spectrometry. Mass spectral interpretation is the method employed to identify the chemical formula, characteristic fragment patterns and possible fragment ions from the mass spectra. The fragmentation pattern is characterized by peaks separated by 14 mass units a ch 2 group. It is, however, more common to use fragmentation rules which are manually curated from mass spectrometry literature by experts. Gas chromatography separates the components of a mixture and. Pdf general fragmentation rules for isomerization and fragmentation processes based on firm thermochemical grounds are presented for. Page 1 of 38 fragmentation pathways of drugs of abuse and their metabolites based on qtof msms and mse accuratemass spectra 5 lubertus bijlsma a, juan v. This section will ignore the information you can get from the molecular ion or ions. Cid results in highly efficient precursor ion fragmentation subject to a low mass cutoff, or the socalled rule. The fragmentation pattern contains clusters of peaks 14 mass units apart which represent loss of ch2nch3. The rule may be extended to fragmentation ions as well. Major fragmentation peaks result from cleavage of the cc bonds adjacent to the.
What are the general rules predicting prominent peaks in a mass spectrum. Compound identification from accurate mass msms spectra is a bottleneck for untargeted metabolomics. Analysis of low mass ions in peptide fragmentation spectra. Mass spectroscopy mass spectroscopy is a technique causing the formation of the gaseous ions with or without fragmentation. The leading scientist in this field was fred mclafferty who together with frantisek turecek has written a very.
So, this peptide gets fragmented into various pieces as you can see here where again mass to charge ratio over the intensity. Tandem mass spectrometry msms dissociation pathways can vary markedly between compound classes and can result in challenging and timeconsuming interpretation of the data. Learn about the agilent atmospheric pressure photoionization source for lcms which combines agilents proven orthogonal spray nebulization and counterflow drying gas with innovative photoionization pioneered by syagen technology. So, first mass analyzer isolates this mass tocharge ratio and sends that on for fragmentation and second, a second mass spec analysis.
Tandem mass spectrometry is an important tool for structure elucidation of natural and synthetic organic products. Definitions of terms relating to mass spectrometry iupac. Atmospheric pressure photoionization source appi agilent. These reactions are well documented over the decades and fragmentation pattern is useful to. Assistant professor department of pharmaceuticcal chemistry dharmaj degree pharmacy college presented by. Fragmentation pathway of drugs of abuse and their metabolites. Sometimes, the ms instruments are even combined with other analytical technologies ion mobility im, ir spectroscopy, etc. 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. These reactions are well documented over the decades and fragmentation pattern is useful to determine the molar weight and structural. Evenelectron ions cannot cleave to a pair of oddelectron fragments from thermodynamics 2.
The reason for the potency of ms is that it is superior to other analytical. Explain rules of fragmentation in mass spectroscopy with one example each. First, the fundamental notions of mass spectrometry are explained, so that the reader. Chapter 2 fragmentation and interpretation of spectra 2.
Ion intensity analysis of postsource decay fragmentation in curved. Journal of pharmaceutical and biomedical analysis 2017, 146, 3747. 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. Tables 2 and 3 convey some basic mass spectrometry information, such as fragment ion structures, occurrence, and how to calculate their masses. Mass spectrometry serves as the best possible technique for the determination or confirmation of molecular weight of compounds. Feb 19, 2015 introduction to ionization and fragmentation in mass spectrometry. Mass spectrometry ms is the dominant analytical technique in metabolomics. Qtof ms library containing 589 accurate mass spectra. Since the charge of an electron is known, the mass to charge ratio a measurement of an ions mass.
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