For higher mass profiles (intact proteomics), we suggest a Pearson correlation of 0.9 or greater, and 0.7 or greater otherwise. Alongside the trelliscope display, the main pipeline exports csv files with molecular formulas and masses, all matched isotope peaks regardless of score, and the processed mass spectra. MS Data. MALDI-MS data from intact protein and tryptic peptide analyses were collected from sections of a fresh-frozen and non-embedded female Sprague Dawley rat brains (Rattus norvegicus). Briefly, tissues were purchased from BioIVT (Westbury, NY) and cryosectioned as 10 𝜇m sections onto either ITO (indium-tin oxide) for MALDI-MS or PEN (polyethylene napthalate)-membrane slides for laser capture microdissection. Briefly, intact proteins were analyzed after a tissue fixation and lipid depletion with a protocol, and tryptic peptides were analyzed after in-situ deposition of trypsin directly on the tissue and overnight incubation, this is described in great depth elsewhere. Glycan data was collected from formalin-fixed paraffin-embedded (FFPE) soybean nodules (Glycine max cv. Williams 82). Briefly, FFPE soybean nodules were cryosectioned as 7 𝜇m sections onto ITO slides, where PNGase was applied and incubated using a protocol described in greater depth elsewhere. Both glycans and intact proteins were analyzed on a custom UHMR Q Exactive HF Orbitrap (Thermo Scientific, Bremen, DE) fitted with an elevated pressure MALDI source (Spectroglyph, Kennewick, WA) operated under a custom privilege license. Tryptic peptides were analyzed on a 12T solariX Fourier transform ion cyclotron resonance mass spectrometer (Bruker Daltonics, Bremen, DE). All raw MALDI-MS data were summed with Mozaic (v.2022.5.1.b1; Spectroswiss, Lausanne, CH). Experimental proteoform/peptide databases were based on LC-MS/MS data from published results of intact and digested 31 LC-MS/MS. All MS Data is included within the R package.