| calculateIons | A function to calculate Y-ions |
| compileData | A function to compile data for the 'data' argument in... |
| defaultIons | A function to define default ion values |
| find_PepPlus | A function to calculate the Y0-ions |
| find_Y0NH3 | A function to calculate the neutral loss of ammonia from a... |
| find_Y1 | A function to calculate the Y1-ions |
| find_Y1Ca | A function to calculate the neutral loss of a carbamidomethyl... |
| find_Y1F | A function to calculate the Y1- plus fucose ion |
| find_Y1Mox | A function to calculate the neutral loss of methane sulfenic... |
| find_Y2 | A function to calculate the Y2-ion |
| find_Y2F | A function to calculate the Y2- plus fucose ion |
| find_Y3 | A function to calculate the Y3-ion |
| find_Y3F | A function to calculate the Y3- plus fucose ion |
| find_Y3FX | A function to calculate the Y3- plus fucose and xylose ion |
| find_Y3X | A function to calculate the Y3 plus xylose-ion |
| glycoChainSaw | A function to modify a chainsaw in silico digest |
| glycoChainSawHRP | A function to modify a chainsaw in silico digest that is like... |
| glycoChange | A function to change N to n for predicted glycosylation sites |
| glycoRQ | A function to estimate relative abunance of glycoforms |
| gPSMvalidator | A function to validate and annotate plant... |
| gPSMvalidatorMaxis | A function to validate and annotate plant... |
| peakplot02 | A function to plot MS data |
| peakplot06 | A function to plot MS data |
| pGlycoFilter | A function to validate a glycan composition prediction |
| PreferredDeltaMasses | A function to add the glycosylation motif for a MyriMatch... |
| psm02 | A function to match peptides to spectra |
| psm06 | A function to match peptides to spectra |
| Read.GlycoMod | A function to import GlycoMod data |
| Read.GlycoMod.maxis | A function to import GlycoMod data from maxis results |
| Read.IDPdb | A function to import IDPicker results |
| Read.IDPdb.maxis | A function to import IDPicker results from maxis data |
| Read.MS2Data | A function to import MS2 binary data generated with msaccess... |
| Read.RQ | A function to import RQ data |
| Read.RQinput | A function to make the RQ input table |
| Read.SICData | A function to import SIC data |
| retentionTimeTable | A function to make a retention time table |
| rt.restrict | A function to filter gPSMs by retention time |
| spectrumTable | A function to calculate monoisotopic precursor mass |
