Imfolio Report
All general practicals and practicals on topic 5 Breath and Faeces analysis (BF,
coordinator name)
Surname Initials
ID: i0000000
Tutorial group 00
BBS2003
Date: 0/0/0000
1
,Table of contents
1. Generating big data from liquid samples using MALDI-ToF Mass
2. Computer PET practical
3. MRI/MRS computer analysis
4. Basic trans-illumination microscopy (bright-field microscopy practical)
5. Data analysis of large data sets
6. Topic 5 practical 1: Big data around us
2
, 1. Generating big data from liquid samples using MALDI-ToF Mass
spectrometry
Introduction:
Biological samples are often analysed to obtain information about their molecular
composition. This can also include their concentrations and their structure. Matrix
associated laser resorption/ionization (MALDI) and Time of flight (ToF) mass
spectrometry is a technique that allows us to carry out such an analysis and obtain
information on non-volatile molecules like proteins, amino acids, sugars and lipids
from saliva samples (1). It is manly used for the acquiring protein profiles. This
technique has remarkable clinical applications, with the diagnosis of diabetes mellitus
being one of them (1). This works by detecting the amount of glucose to one of the
subunits of haemoglobin.
There are three stages involved in MALDI ToF mass spectrometry. First, the sample
of interest, which is mixed with a matrix compound, which crystalizes and secures the
sample in place, before it is irradiated by a laser pulse [2]. The matrix facilitates the
desorption of the sample by absorbing the laser’s energy, thus increasing its
temperature, and carrying the sample molecules into the gas phase [2]. Moreover, the
matrix facilitates the ionization of the sample molecules by exchanging protons with
them and giving them a charge [2]. In the next step, an electric field is applied to the
ions, causing them to accelerate towards an ion detector (2,3). The field applies a
1 2
constant kinetic energy ( K= mu ) to the ions and due to the definition of kinetic
2
energy, the ions with the smallest mass will have a shorter time of flight to the
detector (2,3). From the known electric filed voltage, travel distance and by applying
the rules of energy conservation, the ToF mass spectrometer generates a mass-to-
charge-ratio (m/z) mass spectrum. This is analysed and interpreted to in the last step,
to obtain meaningful results about the initial sample (1).
MALDI has multiple advantages over other techniques. It is a soft ionization
technique, that preserves the sample molecules intact as opposed to other techniques
where there might be fragmentation, which makes the interpretation of the results
challenging (2). Furthermore, MALDI is a method that allows us to analyse large
organic non-volatile that are difficult to ionize in the gas phase. This technique also
has remarkable clinical applications, with the diagnosis of diabetes mellitus being one
of them (1). This works by detecting the amount of glucose to one of the subunits of
haemoglobin via mass spectrometry.
The aim of this practical was to get students acquainted with the principles behind the
MALDI ToF mass spectrometry, as well as for them to generate their own mass
spectrum using their own saliva samples, which would be compared to a control to
interpret the results.
Materials and Methods:
3
All general practicals and practicals on topic 5 Breath and Faeces analysis (BF,
coordinator name)
Surname Initials
ID: i0000000
Tutorial group 00
BBS2003
Date: 0/0/0000
1
,Table of contents
1. Generating big data from liquid samples using MALDI-ToF Mass
2. Computer PET practical
3. MRI/MRS computer analysis
4. Basic trans-illumination microscopy (bright-field microscopy practical)
5. Data analysis of large data sets
6. Topic 5 practical 1: Big data around us
2
, 1. Generating big data from liquid samples using MALDI-ToF Mass
spectrometry
Introduction:
Biological samples are often analysed to obtain information about their molecular
composition. This can also include their concentrations and their structure. Matrix
associated laser resorption/ionization (MALDI) and Time of flight (ToF) mass
spectrometry is a technique that allows us to carry out such an analysis and obtain
information on non-volatile molecules like proteins, amino acids, sugars and lipids
from saliva samples (1). It is manly used for the acquiring protein profiles. This
technique has remarkable clinical applications, with the diagnosis of diabetes mellitus
being one of them (1). This works by detecting the amount of glucose to one of the
subunits of haemoglobin.
There are three stages involved in MALDI ToF mass spectrometry. First, the sample
of interest, which is mixed with a matrix compound, which crystalizes and secures the
sample in place, before it is irradiated by a laser pulse [2]. The matrix facilitates the
desorption of the sample by absorbing the laser’s energy, thus increasing its
temperature, and carrying the sample molecules into the gas phase [2]. Moreover, the
matrix facilitates the ionization of the sample molecules by exchanging protons with
them and giving them a charge [2]. In the next step, an electric field is applied to the
ions, causing them to accelerate towards an ion detector (2,3). The field applies a
1 2
constant kinetic energy ( K= mu ) to the ions and due to the definition of kinetic
2
energy, the ions with the smallest mass will have a shorter time of flight to the
detector (2,3). From the known electric filed voltage, travel distance and by applying
the rules of energy conservation, the ToF mass spectrometer generates a mass-to-
charge-ratio (m/z) mass spectrum. This is analysed and interpreted to in the last step,
to obtain meaningful results about the initial sample (1).
MALDI has multiple advantages over other techniques. It is a soft ionization
technique, that preserves the sample molecules intact as opposed to other techniques
where there might be fragmentation, which makes the interpretation of the results
challenging (2). Furthermore, MALDI is a method that allows us to analyse large
organic non-volatile that are difficult to ionize in the gas phase. This technique also
has remarkable clinical applications, with the diagnosis of diabetes mellitus being one
of them (1). This works by detecting the amount of glucose to one of the subunits of
haemoglobin via mass spectrometry.
The aim of this practical was to get students acquainted with the principles behind the
MALDI ToF mass spectrometry, as well as for them to generate their own mass
spectrum using their own saliva samples, which would be compared to a control to
interpret the results.
Materials and Methods:
3
