Table III Comparison of the results obtained with different MS/MS isolation window widths: ±1.0, ±2.0, ±3.0 and ±4.0 Th
MS/MS scanLys+ and Arg+Spectral cloneMultiplexing ratePSMSuccess rateID efficiency
#%#x#%%
±1.04503788.5797391.774207152.893.4
±2.04402394.21106712.514699942.5106.8
±3.04693796.71675293.575795134.6123.5
±4.04804998.12213134.616362428.7132.4
Unique peptideEffective peptide ID rateaProtein groupEffective protein ID ratebMaxQuant PSMMaxQuant unique peptideMaxQuant protein group
±1.0274550.61039950.088734733246993676
±2.0277770.63140130.091233385237063494
±3.0286230.61041120.087632268226563445
±4.0277160.57740660.084629840211873353
Mean278934047230623492
S.D.506531503136
  • a Unique peptides per MS/MS scan.

  • b Protein groups per MS/MS scan.