Educational algorithms for peak detection in MS spectra

Question

[dan1990]

I will be teaching a course on computational proteomics which covers most post-processing steps of mass-spectrometry data. The students mainly have molecular biology and bioinformatics backgrounds, and therefore not necessarily great programming skills. The course therefore mostly covers concepts and simple algorithms, since the students must implement these during the course.

Thus, I'm looking for simple (not necessarily good) methods for peak detection in a MS spectrum (1D is just fine). The most simple method is of course thresholding and various ways of choosing the threshold, but I think it would be nice to introduce them to a slightly more complex (and biologically relevant) algorithm. I have been unable to find anything in the literature that is not extremely complicated to implement.

In short: I welcome any suggestions for "educational purpose" algorithms for peak detection!

- Dan

Answer 1

[Jean-Karim Heriche]

Here are easy ones. For MS-specific algorithms, this paper provides a good overview of what's involved in practice and could be useful read for the students.

[dan1990]

Thanks! I had not seen the first paper before, but it is very well-written and has a nice level of difficulty for teaching. I already knew the second paper, but I find it poorly written and some of the descriptions of algorithms are misleading and confusing.