# Defining Blood Plasma and Serum Metabolome by GC-MS
## 5 Workflow of GC-MS Analysis of Blood Metabolome
### Mass Spectrometry
#### 5.3.2 Mass Analyzers  
The mass analyzer follows the ion source in the mass spectrometer design. Its task is to measure molecular ions' mass-to-charge ratio (\(m/z\)) and their fragments created at the previous stage. The mass analyzer is followed by an electron multiplier, which, using a cascade of conversion dinoplates, multiplies the number of emission electrons and makes it possible to register an output current of several mA as an analytical signal [152]. GC-MS is a mature technology that uses various types of mass analyzers. The sample preparation carried out before the GC-MS analysis makes the metabolomic fraction of plasma and serum suitable to any mass analyzer, for which there are no design problems with pairing to a gas chromatography system. Further, we describe various mass analyzers (quadrupoles, ion traps, Orbitraps, Fourier transform ion cyclotron resonance mass analyzers, and time-of-flight mass analyzers) with references to relevant experimental projects. Quadrupoles (Q) are the most common analyzers used in GC-MS. The quadrupole mass analyzer consists of four parallel cylindrical metal rods located in a vacuum chamber. An ion moves equidistantly from these electrodes. The magnetic field generated by Q allows only ions with a certain \(m/z\) to pass through. All other ions deviate from a straight path, not reaching the detector. Thus, only one type of ions with a specific \(m/z\) can reach the detector at a time, so the sample is analyzed sequentially by enumerating from the lowest to the highest \(m/z\) ratios. This analyzer is characterized by a wide dynamic range of determined concentrations, high sensitivity but relatively low resolution [12]. In addition, quadrupole mass analyzers have a low scan rate [153; 154], which hampers the deconvolution of overlapping peaks. However, the quadrupole allows for reliable and fast metabolic profiling methods. For example, for the analysis of serum, a method was developed that was practically not inferior in quality to the longer methods. Another competitive advantage of such systems is their reliability and relatively low cost [55; 56]. Often, such analyzers are stacked in tandems of three series-connected quadrupoles (QQQ), which allows you to create complex strategies for targeted metabolomic profiling. The first and third quadrupoles filter the ions passing through them by mass. The second quadrupole is a collision cell that is filled with gas. The operating mode of each quadrupole can be set separately, adjusting the technical performance under the pressure of the need. The mode assumes the passage of ions through the mass analyzer only with a specific pathogen \(m/z\). The scanning mode assumes an alternate change in the \(m/z\) ratio, as a result of which it is possible to capture the spectrum of the entire mass range [155]. One of the options for using the QQQ scheme is the multiple reaction monitoring (MRM) of target metabolites [156]. For instance, using ultra-sensitive gas chromatography-tandem mass spectrometry diclofenac without preliminary derivatization was detected and quantified in blood samples, with a linearity range between 0.1-200 ng/mL, the limit of quantification of 0.1 ng/mL, and the limit of detection of 0.05 ng/mL [157]. Another low-resolution mass analyzer used in targeted metabolomics is the ion trap (IT) [158]. The main advantages of such devices are the elegance of design solutions and ease of operation. Using such a mass analyzer in combination with gas chromatography, it was possible to quantitatively measure the content of 17 steroids in blood plasma [159]. The disadvantages of low-resolution systems are primarily related to the difficulties in determining the structure of unknown compounds. High-resolution detectors include time-of-flight mass analyzers (TOF), Fourier transform ion cyclotron resonance (FT-ICR) instruments, and Orbitraps. FT-ICRs and Orbitraps are also based on trapping ions, but their characteristics differ dramatically from quadrupole mass-analyzers.