Mass chromatogram

The term mass chromatogram refers to the representation of mass spectrometry data as a chromatogram, where the x-axis represents time and the y-axis represents signal intensity. The source data contains mass information; however, it is not graphically represented in a mass chromatogram in favor of visualizing the time and signal intensity data. The most common use of this data representation is when mass spectrometry is used in conjunction with some form of chromatography such as in liquid chromatography-mass spectrometry or gas chromatography-mass spectrometry. In this case the time axis represents the retention time of the analyte identically to traditional chromatography using conventional detection means. The y-axis always represents "signal intensity", however, there are many different types of mass spectrometry experiments that this intensity may represent.

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Selected ion monitoring (SIM)

In the single ion mass chromatogram a small mass window is monitored such that the mass chromatogram represents detection of a very specific mass. Other masses are ignored. This term most often refers to the case where the experiment was designed to achieve this type of data from the beginning. A related term is the extracted ion chromatogram which appears the same however has been reconstructed from a larger data set not exclusively designed to produce a single ion chromatogram. The quality of data from an extracted ion chromatogram is often inferior.

Generally, a mass scan is done first in the range of m/z ratios of interest. This allows for identification of the specific m/z that you want to selectively monitor in SIM mode.

Total ion current (TIC)

The total ion current chromatogram is the opposite of an SIM in that it monitors a very large window often of several hundred mass-to-charge units (the entire range of masses being detected). It is useful in understanding the overall chromatography and hunting for new peaks. In complex samples the TIC can often be fairly useless as so many peaks elute over the run that the peaks are unresolved. The TIC is most often reconstructed after data collection of complete mass spectral data.

Base peak intensity (BPI)

The base peak intensity chromatogram is similar to the TIC however it monitors a small window around only the most intense peak at any one time. This means that the BPI represents the intensity of the most intense peak at every moment in the analysis. BPIs often have a cleaner look than TICs because a lot of the smaller peaks that sum together in a TIC to produce a large background are ignored.

Selected reaction monitoring (SRM)

The SRM is very similar to the SIM experiment except that tandem mass spectrometry is used and a specific product ion of a specific parent ion is detected. Essentially this means that the mass of the analyte is first selected, other ions are filtered away leaving only the analyte ion, this parent analyte ion is then fragmented in the gas phase and then a narrow window of a lower mass fragement ion is monitored and used to make the mass chromatogram. This experiment has very high specificity because the SRM chromatogram represents only ions of a particular mass that fragment in a manner that produce a very specific mass fragment.