New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

3.2. INTRODUCTION TO MALDI TOF MS 25
extract the precise mass/charge (m/z) ratio of the contained peptides and
comprises the steps we named Peak Seeding and Peak Picking.
As will will see in later chapters this approach seems reasonable to us since
the majority of data used in this work 1 is acquired from highly complex protein
mixtures. Most other algorithms are designed to analyze data stemming from
less complex samples. Thus, also the concept of a Peak is slightly different:
in this work we use the peaks found during an analysis to de-convolute larger
peak groups to obtain the original peak patterns representing single peptides.
In data from less complex samples the de-convolution can usually be ommited
and a peak (or a small group of peaks called an isotopica pattern see section
3.4) can typically be identified with a particular peptide.
3.2 Introduction to MALDI TOF MS
Introductory remark: A complete understanding of the internal physical
or (bio-)chemical processes of MALDI does not yet exist, which not only affects
further optimization of MALDI but also renders a full understanding of
the resulting spectra impossible. Poor shot-to-shot and sample-to sample reproducibility
resulting from the crystalline matrix (see below) is another issue
that must be dealt with when interpreting the results. Finally, due to matrix
fragments the MALDI process produces a large amount of ions below m/z 600
(background noise), which makes it impossible to analyze molecules below this
threshold.
History of MS
In the mid-nineteenth century, the physicist Julius Plücker investigated light
emitted in gas-filled tubes (discharge tubes) arising from ionizing the gas by
applying voltage through electrodes at both ends of the tubes.
Later, in 1886, another physicist Eugen Goldstein discovered that discharge
tubes with a perforated cathode emit a glow at the cathode end. Goldstein
concluded that there exists a ray of positive ions passing through the channels
in the cathode, which he called Kanalstrahlen (canal rays).
In 1899 the Nobel Prize laureate Wilhelm Wien (again, physicist) found
that strong electric or magnetic fields deflect these canal rays and constructed
a device with parallel electric and magnetic fields. This device could separate
positive rays according to their charge-to-mass ratio (e/m) and was further
improved consecutively by J.J. Thomson, A.J. Dempster (1918) and F.W.
Aston (1919) to create the first mass spectrograph.
The modern version of these MS machines (we are mainly using in this thesis)
was introduced in 1987 by Franz Hillenkamp and Michael Karas: matrixassisted
laser desorption/ionization mass spectrometry (MALDI-MS).
In 2002, the Nobel Prize in Chemistry was awarded to John B. Fenn for
the development of electrospray ionization (ESI) and Koichi Tanaka for the
development of soft laser desorption (SLD) in 1987.
General Principal
As briefly discussed in section 2.1.1 a modern MALDI-TOF mass spectrometer
contains at least (see Figure 3.2.2)
1 The data is described in detail in section 4.1