| amino_acid_codes | String of valid amino acid codes |
| averageMSD | Generate an average of three MALDI spectrum samples |
| ba_gxy_probs | Calculate the 'GXY' frame of a peptide, and use probabilities... |
| ba_nhyd | Calculate the probability of each possible number of... |
| ba_plotseqpeaks | plot the peaks of a mass spec |
| bioarch_mammal_sequences | Collagen sequences for a range of mammals generated by... |
| bms0.1.2 | EXPERIMENTAL "versioned" copy of bioarch_mammal_sequences |
| corlim_data | Take the output of ms_fit and convert to hits for a range of... |
| corlim_hits | get the hits for a range of correlation limit values |
| corlim_plot | get the hits for a range of correlation limit values |
| dm_cow | Descriminatory peptide markers for cow |
| dm_goat | Descriminatory peptide markers for goat |
| dm_sheep | Descriminatory peptide markers for sheep |
| lag_plot | Plot the lag correction and fit a line to it for a peptide... |
| load.gpm | Load a set of peptides from the Global Protein Machine |
| load.gpm.raw | Load a set of peptides from the Global Protein Machine |
| load.human.markers | Load a set of peptide markers for human |
| load.mcs | Load peptides from the mammalian collagen sequences... |
| load.sample | Load mass spec data from a 2-column space-delimited text file |
| load.sequence | Load sequences from the mammalian collagen sequences... |
| ms_align | Align a theoretical peptide with a mass spec |
| ms_fit | Match a set of peptides with a Mass Spec |
| ms_iso | Obtain the isotope distribution for an amino acid sequence... |
| ms_iso_atom | Obtain the isotope distribution for a molecule consisting of... |
| msms_align | Locally align a pair of mass specs |
| ms_subrange | Get all spectrum data between a mass range |
| ms_tpeaks | Wrapper for the 'R_iso_seq' q2e c function, to get... |
| parse.seq | Parse an amino acid sequence into a set of peptides,... |
| pepcow | All peptides for cow |
| pepgoat | Descriminatory peptide markers for goat |
| pepsheep | Descriminatory peptide markers for sheep |
| peptide.ratio | Get the ratio of ion counts for two peptides |
| pplate | Process a MALDI plate of replicates |
| seq_to_atoms | Calculate the atoms in an amino acid sequence... |
| spp.diffs | get the differences in sequence between two species. NB the... |
| ts_index | Get the species index in the mammalian_collagen_sequences... |
| validseq | This checks if the letters in a sequence are all valid amino... |
| xy.ypos.prolines | count the prolines in the x and y position of a collagen... |
