Mass Spec Terminology
Mass Spectrometry Terminology¶
m/z¶
This is the observed mass to charge ratio of an ion. To be observable in a mass spectrometer, molecules need to have a charge. The m/z is the mass of the molecule divided by the charge. In a lot of cases the charge is 1, so the mass and m/z are the same, but this is not always the case.
Precursor m/z¶
This is the m/z of an intact molecule before it is fragmented. To calculate this, you will need to calculate the monoisotopic mass of the molecule in the neutral form, then figure out which charged particle gives the molecule charge, something like H or Na. Then you will add the mass of this charged particle to mass of the neutral molecule. Then you will divide by the charge to get the precursor m/z of the molecule for that specific ionized form (adduct). This is generally notated as something like M+H or M+Na as examples. To calculate the precursor m/z for different adducts, use the calculator here
Monoisotopic mass¶
The monoisotopic mass is the summed mass of a molecule. However, the mass values for each atom are not the average mass of the atom, but the mass of the most common isotope of that atom. This is because the most common isotope of an atom is the one that is most likely to be observed in nature and in our experiment. For example, the average mass of Carbon (C) is 12.011 Daltons but the mass of the most common isotope C12 is 12 Daltons. In mass spectrometry, it is more useful to use as a starting point the monoisotopic mass.
Mass Spectrometry Data Frames¶
The standard data frame format for the lab is created via MassQL. Using MassQL, there will be two files that are generated:
- MS1 Data Feather/Parquet File with a suffix "_ms1.msql.feather"
- MS2 Data Feather/Parquet File with a suffix "_ms2.msql.feather"
MS1 Data Description¶
This file includes as each row all the MS1 peaks for the entire data file.
- i - This is the intensity of the peak
- i_norm - This is the relative intensity of an MS1 peak within its spectrum. The largest peak will be 1.0
- i_tic_norm - This is the relative intensity of an MS1 peak within a spectrum, where the sum of all peaks within the spectrum will be 1.0
- mz - This is the mass to charge of the peak
- scan - this is the spectrum identifier that a specific peak belongs to. Multiples peaks (rows in the dataframe) belong to a single scan, and multiple scans (thousands to hundreds of thousands) are in each file
- rt - this is retenetion time of the peak
- polarity - 1 means positive, 2 means negative
MS2 Data Description¶
This file includes as each row all the MS2 peaks for the entire data file.
- i - This is the intensity of the peak
- i_norm - This is the relative intensity of an MS1 peak within its spectrum. The largest peak will be 1.0
- i_tic_norm - This is the relative intensity of an MS1 peak within a spectrum, where the sum of all peaks within the spectrum will be 1.0
- mz - This is the mass to charge of the peak
- scan - this is the spectrum identifier that a specific peak belongs to. Multiples peaks (rows in the dataframe) belong to a single scan, and multiple scans (thousands to hundreds of thousands) are in each file
- rt - this is retenetion time of the peak
- polarity - 1 means positive, 2 means negative
- precmz - this is the m/z of the precursor molecule that led to the fragmentation observed in the MS2
- ms1scan - this is the scan number of the precursor ms1 spectrum that directly preceeds the MS2 spectrum
- charge - this is the charge of the precursor molecule