The underlying data here comes from the Ptolemy instrument, a gas chromatograph mass-spectrometer (ion trap, in this case) which can measure ratios of molecules in a range of 14 to 140 Da. (It might also be able to identify somewhat larger species by inducing fragmentation and measuring the resulting pattern of smaller molecules within the effective mass range, but I haven't found if this capability was included).
The article very clearly indicates the data is from COSAC, an instrument on the lander. It also indicates that the sampling came from the "atmosphere" of the comet rather than drilling.
Indeed, good catch - that wasn't in the originally-linked article and I completely overlooked COSAC when looking up the instruments. So here is some info on COSAC:
It is also a GC-MS, but rather than an ion trap, it is a time-of-flight analyzer with a much higher mass range (up to 1500 Da in the widest mode). It is neat to have two mass specs on a single relatively small probe. They are intended to be complementary, as discussed here (briefly, PTOLEMY is designed to measure isotope ratios and the COSAC TOF is designed for organics as it can measure chirality with dual GC columns, and also with a much higher mass range):
[edit: for anyone else interested in mass-spec, I found some slides with an overview of MS instruments on previous probes - I was familiar with several, but there have been many more than I realized: http://jfsm2012.sciencesconf.org/conference/jfsm2012/pages/C...]
Some more info here: http://www.lpi.usra.edu/meetings/lpsc2006/pdf/1937.pdf
and: http://sci.esa.int/rosetta/31445-instruments/?fbodylongid=89...
The instrument has its own Twitter feed, of course: https://twitter.com/philae_ptolemy