Editing Mass spectrum (section)

==Y-axis: signal intensity==
The [[y-axis|''y''-axis]] of a mass spectrum represents signal intensity of the ions.  When using counting detectors the intensity is often measured in counts per second (cps).  When using analog detection electronics the intensity is typically measured in volts.  In [[FTICR]] and [[Orbitrap]]s the [[frequency domain]] signal (the ''y''-axis) is related to the [[Power (physics)|power]] (~amplitude squared) of the signal [[sine wave]] (often reduced to an [[rms power]]); however, the axis is usually not labeled as such for many reasons.  In most forms of mass spectrometry, the intensity of ion current measured by the spectrometer does not accurately represent relative abundance, but correlates loosely with it. Therefore, it is common to label the ''y''-axis with "arbitrary units".

===Y-axis and relative abundance===
Signal intensity may be dependent on many factors, especially the nature of the molecules being analyzed and how they ionize. The efficiency of ionization varies from molecule to molecule and from ion source to ion source. For example, in electrospray sources in positive ion mode a quaternary amine will ionize exceptionally well whereas a large hydrophobic alcohol will most likely not be seen no matter how concentrated. In an EI source these molecules will behave very differently. Additionally there may be factors that affect ion transmission disproportionally between ionization and detection.

On the detection side there are many factors that can also affect signal intensity in a non-proportional way. The size of the ion will affect the velocity of impact and with certain detectors the velocity is proportional to the signal output. In other detection systems, such as [[FTICR]], the number of charges on the ion are more important to signal intensity. In [[Fourier transform ion cyclotron resonance]] and [[Orbitrap]] type mass spectrometers the signal intensity (Y-axis) is related to the amplitude of the [[free induction decay]] signal. This is fundamentally a power relationship (amplitude squared) but often computed as an [rms]. For decaying signals the rms is not equal to the average amplitude. Additionally the damping constant (decay rate of the signal in the fid) is not the same for all ions. In order to make conclusions about relative intensity a great deal of knowledge and care is required.

A common way to get more quantitative information out of a mass spectrum is to create a standard curve to compare the sample to. This requires knowing what is to be quantitated ahead of time, having a standard available and designing the experiment specifically for this purpose. A more advanced variation on this is the use of an [[internal standard]] which behaves very similarly to the analyte. This is often an isotopically labeled version of the analyte. There are forms of mass spectrometry, such as [[accelerator mass spectrometry]] that are designed from the bottom up to be quantitative.

===Spectral skewing===
'''Spectral skewing''' is the change in relative intensity of mass spectral peaks due to the changes in concentration of the [[analyte]] in the [[ion source]] as the mass spectrum is scanned. This situation occurs routinely as [[Chromatography|chromatographic]] components [[Elution|elute]] into a continuous ion source.<ref>Watson, J. THrock, Sparkman, O David.Introduction to Mass Spectrometry.John Wiley & Sons, Inc. 4th Edition, 2007. Page:113</ref> Spectral skewing is not observed in [[ion trap]] ([[Quadrupole ion trap|quadrupole]] (this has been seen also in [[Quadrupole mass spectrometer|QMS]]) or magnetic) or [[Time-of-flight mass spectrometry|time-of-flight]] (TOF) [[mass analyzer]]s because potentially all [[ion]]s formed in operational cycle (a snapshot in time) of the instrument are available for detection.