Quantitative Proteomics Bibliography

Here are some of the first SILAC papers - primarily from our lab.

(1) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Mol Cell Proteomics. 2002 May;1(5):376-86.

Shao-En Ong, Blagoy Blagoev, Irina Kratchmarova, Dan Bach Kristensen, Hanno Steen, Akhilesh Pandey, and Matthias Mann.

- *** First initial SILAC publication in mammalian cell culture.  Describes the use of deuterated leucine (leu-d3) specifically for quantitation of proteins from two cell states - undifferentiated myoblasts and differentiated myotubes.  MS analyses with nanoelectrospray hybrid ESI-QTOF and MALDI.

(2) Properties of ¹³C-Substituted Arginine in Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)
Web Release Date: 13-Dec-2002; (Article) DOI: 10.1021/pr0255708 

Ong SE, Kratchmarova I, and Mann M

- ** Describes the use of 13C-labelled arginine (Arg-13C6) in SILAC for quantitative proteomics with LC-MS.  Co-elution of both unlabelled and labelled peptides provides highly accurate analyses with multiple datapoints for quantitation of even single peptides.

(3) Mass spectrometric-based approaches in quantitative proteomics.
Methods 2003 Feb;29(2):124-30

Ong SE, Foster LJ, Mann M.

- A general review of the SILAC approach compared with other quantitation approaches.  Strengths and limitations of the various quantitation methods are outlined. Discussion of the benefits of labeling with arginine and lysine for full quantitative coverage.

(4) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. 

Nature Biotechnol 2003 Mar, 21(3):315-8.  (View the PDF)

Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M.

- *** First 'real' biological application of SILAC.  The labelling allows the distinction of true interaction binders to a bait from non-specific interactions.   Quantitation of 228 proteins.  28 proteins clearly implicated in EGF signaling with many well known players in the pathway found with high differential ratios. 

(5) Mass spectrometry-based proteomics.
Nature 2003 Mar 13;422(6928):198-207

Aebersold R, Mann M.

- A good overview of quantitative proteomics with perspectives for future directions, new MS equipment etc.

(6) Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors.
Proc Natl Acad Sci U S A 2003 Apr 30;

Foster LJ, De Hoog CL, Mann M

- ** Comparison of different lipid raft preparations with or without a cholesterol-disrupting drug along with SILAC allows the identification of specific raft factors.

(7) Hystag - a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain.
Mol Cell Proteomics. 2003 Nov 10 

Olsen JV, Andersen JR, Nielsen PA, Nielsen ML, Figeys D, Mann M, Wisniewski JR.
 

- ** The Hystag is introduced! A quantitative tag bearing a 6xHis tag, a Trypsin cleavage site, Alanine-Deu4 and a sulfhydryl-reactive group is actually a 10-mer peptide.  It has many desirable properties which make it easy to synthesize with a standard peptide synthesizer.

(8) A novel proteomic screen for peptide-protein interactions

J Biol Chem. 2003 Dec 16.

Schulze WX, Mann M.

- ** Peptides (phosphorylated or non-phosphorylated) are used to probe cell lysates for interacting proteins.  High quantitation accuracy from SILAC allows the discrimination of real interactions from unspecific binders.