I've been working with mass spectrum data analysis (but my field is computer science).
I'm using a library that allows me to get the entire Mass Intensity of the MS1 scan (such as [time, intensity]). However, by searching for the highest value for intensity, it is always a few integers lower than the base peak intensity.
I'm retrieving the information from a mzXML file, and the library that I'm using is ms-data-core-api. The method used to retrieve the intensity map, in case anyone has ever used this library, is this one: public double getMassIntensityMap(). I retrieve the highest peek in the map by iterating the matrix returned and updating a variable with the highest value found in the
y axis (given
double [x = time][y = mass].
Examples of the difference of data include the following:
scan 1 (MS1): Highest peak in map: 789991.875 / base peak intensity: 793728.0 scan 2 (MS1): Highest peak in map: 714475.5 / base peak intensity: 719125.0 scan 3 (MS1): Highest peak in map: 673152.6875 / base peak intensity: 680567.0
From what I can tell, the instrument used for these scans is a fourier transform ion cyclotron resonance mass spectrometer, using Xcalibur as the software.
Does this makes sense, and why?