| Name | Lines of code | Maintainability | Test coverage |
| lib/mspire/mzml/index_list.rb | 76 | A 0 mins | |
| lib/mspire/ident/pepxml/search_hit.rb | 84 | A 0 mins | |
| lib/mspire/ident/pepxml.rb | 87 | A 2 hrs | |
| lib/mspire/imzml/writer/commandline.rb | 91 | A 2 hrs | |
| lib/mspire/quant/qspec.rb | 110 | A 3 hrs | |
| lib/mspire/cv/paramable.rb | 110 | A 1 hr | |
| lib/mspire/mzml/spectrum.rb | 114 | A 4 hrs | |
| lib/mspire/digester.rb | 116 | A 1 hr | |
| lib/mspire/spectrum_like.rb | 117 | A 45 mins | |
| lib/mspire/plms1.rb | 118 | A 25 mins | |
| lib/mspire/mzml/reader.rb | 120 | A 2 hrs | |
| lib/mspire/ident/pepxml/sample_enzyme.rb | 121 | A 1 hr | |
| lib/mspire/mzml.rb | 125 | A 3 hrs | |
| lib/mspire/mzml/data_array.rb | 131 | B 6 hrs | |
| lib/mspire/paramable.rb | 137 | A 1 hr | |
| lib/mspire/ident/peptide/db/creator.rb | 206 | D 1 day | |
| lib/mspire/peaklist.rb | 236 | C 1 day | |
| lib/mspire/imzml/writer.rb | 304 | D 2 days |