Two datasets corresponding to the spectral type (CID, Low, Standard, αLP) and (ETD, Low, Standard, αLP) contain 49,167 spectra each. These datasets were generated in the Komives laboratory (University of California, San Diego). The detailed experimental procedures to generate these datasets are as follows. Wild-type S. pombe cells were lysed in: 50mM Tris-HCl pH: 8.0; 150mM NaCl; 5mM EDTA; 10% Glycerol; 50mM NaF; 0.1mM Na3VO4; 0.2% NP40 and stored at −80°C. The debris was pelleted and then the supernatant was collected. The pellet was extracted according to [56 (link)]. Briefly, the pellet was resuspended in 200 ul of 0.1 M NaOH, 0.05 M ETDA, 2% SDS, and 2% beta-mercaptoethanol and incubated at 90°C for 10 minutes. Acetic acid was added to 0.1M and vortexed followed by an additional incubation at 90°C for 10 minutes before clarification by centrifugation and Methanol/chloroform extraction. The pellet was resuspended in 100 mM Tris containing 0.1% sodium deoxycholate with TCEP at 5 mM. Free thiols were capped with n-ethylmaleimide. Excess reagent was removed by ultrafiltration with amicon-4 10 kDa centrifugal devices. The protein was then quantified and exchanged into 6M guanidine for digestion overnight by αLP. The digests were quenched by the addition of formic acid to 1%, followed by desalting by sep-pak (Waters, Milford, MA). Peptides were then fractionated with Electrostatic Repulsion-Hydrophilic Interaction Chromatography [57 (link)]. Fractions were assayed for protein concentration using a BCA assay and pooled into 18 fractions of equal protein concentration, evaporated to dryness and resuspended in 100 uL of 0.2% FA. Nano liquid chromatography tandem mass spectrometry (nLC-MS/MS) was performed with a LTQ XL mass spectrometer equipped with ETD. 10 ul of each fraction (≈ 1 ug) was injected onto a 12 cm × 75 um I.D.C18 column prepared in house and eluted in 0.2% FA with a gradient of 5% to 40% ACN over 60 min followed by wash and re-equilibration totaling 90 minutes of MS data per run. The flow was split about 1:500 to a flow rate of about 250 nL/min. A survey scan was followed by data dependent fragmentation of the 4 most abundant ions with both CID and ETD with supplemental activation. The maximum MS/MS ion accumulation time was set to 100 ms. Fragmented precursors were dynamically excluded for 45 seconds with one repeat allowed.