Basic Design of MRM Assays for Peptide Quantification - LC-MS/MS in Proteomics: Methods and Applications - page 183

(e) Chemical labeling (SILAC, iTRAQ, TMT) can be of great
help by permitting the simultaneous analysis of multiple
conditions within the same sample. However, labeling effi-
ciency should be taken into account.
(f) Limit of detection and limit of quantification are important
standards to obtain comparable data sets. Limit of detection
(LOD): signal-to-noise should be above or equal to 3. Limit
of quantification (LOQ): signal-to-noise should be above or
equal to 10.

Acknowledgments

The authors would like to thank Tony Pawson, Brett Larsen,
Vivian Nguyen, Ginny Chen, Rune Linding, Steve Tate, Sarah
Robinson, and Marilyn Hsiung for helpful discussion, support,
and advice. Claus Jorgensen would like to thank the Lundbeck
Foundation for generous support.

References

1. Lange, V., Picotti, P., Domon, B., and Aeber-
sold, R. (2008) Selected reaction monitoring
for quantitative proteomics: a tutorial. Mol.
Syst. Biol. 4 (222), 1-14.
2. Keshishian, H., Addona, T., Burgess, M.,
Kuhn, E., and Carr, S. A. (2007) Quanti-
tative, multiplexed assays for low abundance
proteins in plasma by targeted mass spec-
trometry and stable isotope dilusion. Mol.
Cell Proteomics 6 (12), 2212-2229.
3. Keshishian, H., Addona, T., Burgess, M.,
Mani, D. R., Shi, X., Kuhn, E., Sabatine, M.
S., Gerszten RE., Carr SA. (2009) Quantifi-
cation of cardiovascular biomarkers in pateint
plasma by targeted mass spectrometry and
stable isotope dillusion. Mol. Cell Proteomics
8 (10), 2339-2349.
4. Addona, T., Abbatiello, S. E., Schilling, B.,
Skates, S. J., Mani, D. R., Bunk, D. M.,
Spiegelman, C. H., Zimmerman, L. J., Ham,
A. J., Keshishian, H., Hall, S. C., Allen, S.,
Blackman, R. K., Borchers, C. H., Buck, C.,
Cardasis, H. L., Cusack, M. P., Dodder, N.
G., Gibson, B. W., Held, J. M., Hiltke, T.,
Jackson, A., Johansen, E. B., Kisinger, C. R.,
Li, J., Mesri, M., Neubert, T. A., Niles, R. K.,
Pulsipher, T. C., Ransohoff, D., Rodriguez,
H., Rudnick, P. A., Smith, D., Tabb, D.
L., Tegeler, T. J., Variyath, A. M., Vega-
Montoto, L. J., Wahlander, A., Waldemar-
son, S., Wang, M., Whiteaker, J. R., Zhao,

L., Anderson, N. L., Fisher, S. J., Liebler, D.
C., Paulovich, A. G., Regnier, F. E., Tempst,
P., Carr, S. A. (2009) Multi-site asessment
of the precision and reproducibility of multi-
ple rection monitoring-based measurements
of proteins in plasma. Nat. Biotechnol. 27 (7),
633-641.
5. Wolf-Yadlin, A., Hautaniemi, S., Lauffen-
burger, D. A., and White, F. M. (2007)
Multiple reaction monitoring for robust
quantitative proteomic analysis of cellular
signaling networks. Proc. Natl. Acad. Sci.
USA 104 (14), 5860-5865.
6. Mayya, V., Rezual, K., Wu, L., Fong,
M. B., and Han, D. K. (2006) Abso-
lute quantification of multisite phospho-
rylation by selective reaction monitor-
ing mass spectrometry: determination of
inhibitory phosphorylation ststus of cyclin-
dependent kinases. Mol. Cell Proteomics 5 (6),
1146-1157.
7. Picotti, P., Bodenmiller, B., Mueller, L. N.,
Domon, B., and Aebersold, R. (2009) Full
dynamic range proteome analysis of S. cere-
visiae by targeted proteomics. Cell 138 (4),
795-806.
8. Fusaro, V. A., Mani, D. R., Mesirov, J. P.,
and Carr, S. A. (2009) Prediction of high-
responding peptides for targeted protein
assays by mass spectrometry. Nat. Biotechnol.
27 (2), 190-198.