methods and any associated references are available in the online version of the paper at http://www.nature.com / naturemethods/.
difference in optimal collision energies for identification and quantification supplementary note real - time filtering supplementary table 1 summary of quantification and identification results supplementary protocol implementing quantmode on commercial mass spectrometers
 we describe a mass spectrometry method , quantmode , which improves the accuracy of isobaric tag  based quantification by alleviating the pervasive problem of precursor interference  
 co - isolation of impurities  through gas - phase purification . 
 quantmode analysis of a yeast sample  
 contaminated with interfering human peptides showed substantially improved quantitative accuracy compared to a standard scan , with a small loss of spectral identifications . 
 this technique will allow large - scale , multiplexed quantitative proteomics analyses using isobaric tagging . 
METHODS
Supplementary Material