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. Author manuscript; available in PMC: 2013 May 15.
Published in final edited form as: Anal Chem. 2012 May 3;84(10):4535–4543. doi: 10.1021/ac300510t

Figure 3. IsoQuant overcomes the limitation of under-sampling in data-dependent instrument methods, thereby increasing the accuracy of SILAC-based quantitation.

Figure 3

A) Extracted ion chromatogram (XIC) of 572.77 m/z (SILAC heavy-labeled peptide). 572.77 m/z was selected for MS2 fragmentation and was identified by SEQUEST in the first two scans (indicated by *; retention time (RT) 32.70 min and 32.75 min). B) MS1 scan at RT 32.70 min (568.0 – 575.0 m/z) demonstrating an incomplete isotope envelope of 569.76 m/z (SILAC light-labeled peptide). C) MS1 spectrum from the most intense peak in A) at RT 32.84 min. Although 572.77 m/z was not selected for MS2 fragmentation due to dynamic exclusion, its complete isotopic envelope permitted quantitation by IsoQuant.