Table III Comparison of trypsin-based digestion protocols after analysis by label-free quantitative nanoLC-MSE
Digestion protocolPeptide identificationsProtein identifications
Averagea (sd)ID1 (≥2)bID2 (≥2)cAveragedpI (≥2)Averaged GRAVY (≥2)Averagea (sd)Quantified1 (≥2)bQuantified2 (≥2)cAveraged MW (kDa)Averaged coveragePeptides/Protein 1b–2c
ISD:RG (AP)2584 (56)186934526.42−0.19246 (9)22632745.730.48.3–10.6
ISD:Urea2502 (95)172935366.55−0.22222 (9)20433146.733.98.5–10.7
ISD:SDC (AP)2782 (129)208735596.44−0.15261 (9)24533144.532.28.5–10.8
ISD:SDC (PT)3144 (295)239436966.50−0.18262 (15)23933646.736.910.0–11.0
SF-ISD:SDC (AP)3020 (119)229335746.45−0.13257 (13)24432844.535.09.4–10.9
SF-ISD:SDC (PT)3453 (63)270636266.35−0.16287 (5)27233445.638.29.9–10.9
  • a Average number of unique peptide sequences or protein identifications from three replicates.

  • b Number of unique peptide sequences or proteins identified by PLGS in at least two out of three replicates.

  • c Number of unique peptide sequences or proteins identified in at least two out of three replicates after run-alignment (Progenesis LC-MS).

  • d Averaged values are calculated from peptides and proteins present in at least two out of three replicates.