# Base Peak Intensity different than higher value in Mass Intensity Map

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?

• @CurtF. I'm sorry, I should have added this information in the first place. I'll update the question. – streppel Jun 28 '16 at 4:08