The development of LC-MS/MS instruments and related applications improved the large-scale analyses of proteins and peptides in complex biological mixtures. The historical factor limiting these types of studies was the lack of sensitivity and reproducibility. However, the capacity of these analyses to detect proteins and peptides was significantly enhanced to a point where they are routinely performed in specialized laboratories in support to drug development programs as well as prognostic and diagnostic investigations. The analytical strategy used in peptidomic analyses needs to minimize the fluctuation in data measurements that might mask or reduce the precision of the determinations and consequently reduce the sensitivity of the assay. Inherently, it outlines the importance of careful standardization to reduce technical and instrumental variation. Therefore, this review will focus on the strengths and the limitations of the different experimental approaches used for the integration of internal standards in peptidomic studies. This review will examine a wide variety of methods, reagents, instrumentations and data analysis tools available to design peptidomic experiments. Moreover, this review will focus on the importance of precision and accuracy in order to adequately establish analysis threshold to detect peptide expression differences. Copyright © 2012 John Wiley & Sons, Ltd.