MASS SPECTROMETRY

Course objectives

The lectures are aimed to provide to the students an educational path starting from the basic concepts of mass spectrometry up to its last developments and applications in the fields of analytical chemistry and biomolecules study. At the end of the course, the students have to demonstrate the knowledge of the theory and basic principles of mass spectrometry, as well as of the various ionization techniques and mass analyzers. Moreover, the students should have understood the potential of the coupling between liquid or gas chromatography and mass spectrometry, as well as tandem mass spectrometry, in particular concerning complex mixtures and compounds at trace levels. Furthermore, the students have to be able to extrapolate and describe the main data and information obtainable from a mass spectrum. Concerning the application of the knowledge, in case of a real problem, the students should possess the capability of select both the most suitable instrumentation and acquisition modes for the analysis of biological, environmental, and food samples. The capability of arguing the choice of possible analytical strategies is another important objective. Finally, self-study capability should be proven by gaining further insight into specific course topics with the aid of the scientific literature. The aims of the course are described in detail according to the five Dublin descriptors. Dublin Descriptor 1 – Knowledge and understanding At the end of the course, the students have learned the basic theoretical principles of mass spectrometry, as well as of the various ionization techniques and the main mass analyzers. The students have to know the theory of tandem mass spectrometry and understand the possibilities concerning both qualitative and quantitative determination. They have to understand the potential of the coupling of tandem mass spectrometry with separative techniques or the possibility of very fast “in situ” analyses. They have to recognize between information obtainable from low- and high-resolution mass spectrometry and to understand the concept of mass accuracy. Dublin Descriptor 2 - Applying knowledge and understanding The students have to acquire the capability of facing a complex analytical problem with the aid of mass spectrometry and tandem mass spectrometry, for example for applications in environmental or food analysis. It is important also to take into account the related European law concerning the maximum allowable limits of certain substances depending on the limit of detection of the technique and its various acquisition modes. The students have to be able to select the most suitable ionization technique depending on target analytes and sample origin, also suggesting a possible coupling between mass spectrometry and a separation technique. Dublin Descriptor 3 - Making judgments The students have to develop the capability of critical evaluation concerning an analytical or general research problem, which requires the application of mass spectrometry, by connecting the knowledge acquired during the whole study course. This capability is developed by the aid of examples from the scientific literature, with particular emphasis on complex mixtures of compounds present at trace level and/or structurally unknown, and biomolecules (e.g. proteins and peptides). It is also important the capability of justifying the choice of the analytical strategy. Dublin Descriptor 4 – Communication skills The students have to be able to write in a report or verbally communicate the acquired knowledge, in a concise, coherent, and well-focalized way, also by the aid of graphic informatic tools, to be understandable by both specialized and non-specialized audience. Dublin Descriptor 5 – Learning skills At the end of the course, the students should have developed suitable tools to stimulate detailed studies and links between different topics. They should possess the skills to independently refer to the scientific literature related to mass spectrometry to deepen both some theoretical aspects and, most of all, application aspects. By referring to the scientific literature, the students have to be able to obtain the information to solve new problems, as well as to get the fundamental tools useful for their professional activity.

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CHIARA CAVALIERE Lecturers' profile

Program - Frequency - Exams

Course program
1) Brief history and recent developments of mass spectrometry. Basic principles and various chemical application fields of mass spectrometry. Mass spectrometer components. Introduction to mass spectrometry techniques and general principles. Mass spectrum and its representation. Atomic mass unit; definitions of nominal mass, average mass, and monoisotopic mass. Mass resolution and mass accuracy, isotopic distribution. Isotope pattern calculation for mass spectrum interpretation. (4 hours). 2) Ion sources: hard and soft ionization techniques. Chemical ionization (CI). Desorption ionization techniques. Matrix-assisted laser desorption ionization (MALDI) and its modifications. Atmospheric pressure ionization: electrospray (ESI), nanoESI, atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI). Ambient ionization techniques: desorption ESI (DESI) and direct analysis in real-time (DART). Fundamental rules for ion formation and fragmentation. (16 hours) 3) Mass analyzers. Quadrupole, ion guides, and collision cells. Paul and linear ion traps (3D versus 2D), ion ejection by stability limit and by resonance. Time of flight with reflectron and delayed extraction; orthogonal acceleration. Magnetic and electromagnetic sector. Fourier transform mass spectrometry: Orbitrap and ion cyclotron resonance mass analyzers. Hybrid instruments. Dependence of resolution from mass to charge ratio. Detectors and data acquisition. (20 hours) 4) Coupling of mass spectrometry with liquid and gas chromatography techniques. (2 hours) 5) Fragmentation reactions by collision-induced dissociation (CID) activation. Tandem mass spectrometry, scan modes. Applications and quantitative analysis. Concepts of CID fragmentation: high and low energy collision. Application of mass spectrometry techniques to the analysis of biomolecules: peptide and protein fragmentation. Other activation techniques: electron capture or transfer dissociation (ECD/ETD). (6 hours)
Prerequisites
Student with a Bachelor degree in Chemistry possesses the competences to attend and understand the course syllabus
Books
- Edmond de Hoffmann and Vincent Stroobant, Mass spectrometry, Principles and Applications. Ed. Wiley, 3rd edition (2007). - Jürgen H. Gross. Mass Spectrometry. A textbook, second edition. Ed. Springer - Teaching and didactic materials available on Moodle https://elearning2.uniroma1.it/ - Some optional publications on specific subjects will be suggested by the teacher
Teaching mode
The course is mainly carried out in the class to provide the student with basic knowledge of mass spectrometry and understand its application capacities (in agreement with the educational goals) with some practical examples, and involving the student to participate with questions during the lesson. The last applications of mass spectrometry for the study of biomolecules are described, in particular illustrating metabolomics and proteomics sciences. The exercises in class allow the student to verify the applicability of his/her knowledge.
Frequency
Class lesson attendance is not mandatory but strongly recommended.
Exam mode
At the end of the course, the student will be evaluated through an oral exam. During the exam, the student has to demonstrate comprehension of the main topics of the course. The questions will be about the basic principles of mass spectrometry, the ionization techniques, and the mass analyzers, as well as about mass spectrometry applications. Often, the student will be invited to make comparisons between the various ionization sources, between the main features of different mass analyzers, and between the available activation techniques for ion fragmentation. Furthermore, the student should argue with practical examples (suggested by himself and/or by the teacher) which are the best strategies in applying the mass spectrometry techniques. A positive evaluation will be also motivated by the capabilities of reasoning and linking between course topics, as well as by clarity in exposition and communicative appropriateness and correctness of scientific speech. To summarizing, in the choice of the final mark the following features are considered: 1. evidence of full comprehension of the main topics of the course; 2. clarity and completeness in the oral presentation of the contents of the course; 3. reasoning capacity; 4. critical evaluation capacity of a problematic determination of substances by mass spectrometry; 5. capacity of linking contents from different topics. To obtain the highest mark, i.e., 30/30 cum laude, the student has to demonstrate an excellent knowledge of all the topics of the course, but most of all, the student has to be able to link logically and coherently all the arguments.
Bibliography
Some optional pubblications on specific subjects are suggested by the teacher
Lesson mode
The course is carried out in the class to provide the student with basic knowledge of mass spectrometry and its application capacities (in agreement with the educational goals) with some practical examples, and involving the student to participate with questions during the lesson. The most recent applications of mass spectrometry for the study of biomolecules are described, in particular metabolomics and proteomics sciences. Class lesson attendance is not mandatory but strongly recommended.
CHIARA CAVALIERE Lecturers' profile

Program - Frequency - Exams

Course program
1) Brief history and recent developments of mass spectrometry. Basic principles and various chemical application fields of mass spectrometry. Mass spectrometer components. Introduction to mass spectrometry techniques and general principles. Mass spectrum and its representation. Atomic mass unit; definitions of nominal mass, average mass, and monoisotopic mass. Mass resolution and mass accuracy, isotopic distribution. Isotope pattern calculation for mass spectrum interpretation. (4 hours). 2) Ion sources: hard and soft ionization techniques. Chemical ionization (CI). Desorption ionization techniques. Matrix-assisted laser desorption ionization (MALDI) and its modifications. Atmospheric pressure ionization: electrospray (ESI), nanoESI, atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI). Ambient ionization techniques: desorption ESI (DESI) and direct analysis in real-time (DART). Fundamental rules for ion formation and fragmentation. (16 hours) 3) Mass analyzers. Quadrupole, ion guides, and collision cells. Paul and linear ion traps (3D versus 2D), ion ejection by stability limit and by resonance. Time of flight with reflectron and delayed extraction; orthogonal acceleration. Magnetic and electromagnetic sector. Fourier transform mass spectrometry: Orbitrap and ion cyclotron resonance mass analyzers. Hybrid instruments. Dependence of resolution from mass to charge ratio. Detectors and data acquisition. (20 hours) 4) Coupling of mass spectrometry with liquid and gas chromatography techniques. (2 hours) 5) Fragmentation reactions by collision-induced dissociation (CID) activation. Tandem mass spectrometry, scan modes. Applications and quantitative analysis. Concepts of CID fragmentation: high and low energy collision. Application of mass spectrometry techniques to the analysis of biomolecules: peptide and protein fragmentation. Other activation techniques: electron capture or transfer dissociation (ECD/ETD). (6 hours)
Prerequisites
Student with a Bachelor degree in Chemistry possesses the competences to attend and understand the course syllabus
Books
- Edmond de Hoffmann and Vincent Stroobant, Mass spectrometry, Principles and Applications. Ed. Wiley, 3rd edition (2007). - Jürgen H. Gross. Mass Spectrometry. A textbook, second edition. Ed. Springer - Teaching and didactic materials available on Moodle https://elearning2.uniroma1.it/ - Some optional publications on specific subjects will be suggested by the teacher
Teaching mode
The course is mainly carried out in the class to provide the student with basic knowledge of mass spectrometry and understand its application capacities (in agreement with the educational goals) with some practical examples, and involving the student to participate with questions during the lesson. The last applications of mass spectrometry for the study of biomolecules are described, in particular illustrating metabolomics and proteomics sciences. The exercises in class allow the student to verify the applicability of his/her knowledge.
Frequency
Class lesson attendance is not mandatory but strongly recommended.
Exam mode
At the end of the course, the student will be evaluated through an oral exam. During the exam, the student has to demonstrate comprehension of the main topics of the course. The questions will be about the basic principles of mass spectrometry, the ionization techniques, and the mass analyzers, as well as about mass spectrometry applications. Often, the student will be invited to make comparisons between the various ionization sources, between the main features of different mass analyzers, and between the available activation techniques for ion fragmentation. Furthermore, the student should argue with practical examples (suggested by himself and/or by the teacher) which are the best strategies in applying the mass spectrometry techniques. A positive evaluation will be also motivated by the capabilities of reasoning and linking between course topics, as well as by clarity in exposition and communicative appropriateness and correctness of scientific speech. To summarizing, in the choice of the final mark the following features are considered: 1. evidence of full comprehension of the main topics of the course; 2. clarity and completeness in the oral presentation of the contents of the course; 3. reasoning capacity; 4. critical evaluation capacity of a problematic determination of substances by mass spectrometry; 5. capacity of linking contents from different topics. To obtain the highest mark, i.e., 30/30 cum laude, the student has to demonstrate an excellent knowledge of all the topics of the course, but most of all, the student has to be able to link logically and coherently all the arguments.
Bibliography
Some optional pubblications on specific subjects are suggested by the teacher
Lesson mode
The course is carried out in the class to provide the student with basic knowledge of mass spectrometry and its application capacities (in agreement with the educational goals) with some practical examples, and involving the student to participate with questions during the lesson. The most recent applications of mass spectrometry for the study of biomolecules are described, in particular metabolomics and proteomics sciences. Class lesson attendance is not mandatory but strongly recommended.
  • Lesson code10612084
  • Academic year2024/2025
  • CourseChemistry
  • CurriculumChimica dei Sistemi Biologici
  • Year2nd year
  • Semester1st semester
  • SSDCHIM/01
  • CFU6
  • Subject areaDiscipline chimiche analitiche e ambientali