Proteomics – Chemical Labeling – Peptide Synthesis

Peptide Synthesis

Targeted mass spectrometry (MS) isotope analysis (i.e., selected or multiple reaction monitoring, SRM or MRM) is an alternative to antibody-based assays for the verification/validation of putative protein biomarkers, but it also has been employed for discovery-based proteomics (see example references below). One obstacle of this strategy is that every peptide possesses unique biochemical characteristics. Its amino acid composition and possible post-translational modifications defines its elution profile from the liquid chromatography column, ionization, and fragmentation. For developing a clinically relevant MS assay, these peptide properties must be characterized with a synthesized peptide before analyzing the peptide of interest in vivo. The synthesis of labeled peptides is aided by the use of isotope-enriched protected amino acids or preloaded resins in solid phase productions. Absolute quantitation of peptides/proteins in biological samples can then be achieved by application of these heavy peptides.

Stable Isotope-Labeled Peptides and Protein Reagents/Kits

Related Products

Peptide Synthesis Materials view all

❛❛The commercial availability of stable isotope-labeled amino acids with very high isotopic purity has revolutionized quantitative proteomics. From their use in metabolic labeling of cells and rodents for differential discovery proteomics, to their use in synthetic peptides as internal standards for targeted analysis of proteins, isotopically labeled amino acids make it possible to measure, with very high precision, changes in the levels of peptides and the proteins they are derived from in highly complex samples such as cell lysates, tissue, and plasma. Cambridge Isotope Labs has been and continues to be a leader in the commercial production of labeled amino acids and other labeled compounds.❜❜

– Stephen A. Carr, PhD | Senior Director of Proteomics, Broad Institute of MIT and Harvard

Frequently Asked Questions

Does CIL provide catalog and custom-labeled peptides? A few stable isotope-labeled peptides are available off-the-shelf (e.g., oxidized and reduced glutathione). CIL is pleased to supply highly enriched and pure amino acids (both free and protected) to the world’s leading peptide manufacturers for synthesis activities, but does not custom synthesize peptides in-house.

Would 0.8 mM of lysine or arginine preloaded resins provide approximately 8 synthesis at 0.1 mM scale?Yes, theoretically 0.8 mM of resin would provide 8 synthesis at 0.1 mM scale. Final yields are always dependent on actual sequence and the efficiency of the couplings.

Does CIL provide catalog and custom preloaded resins? Yes. Through collaboration with BioSynth, CIL is pleased to offer synthesis-ready preloaded resins. For a list of our catalog offerings, please refer to our Preloaded Resins flyer.

Example References

Novikova, S.E.; Tolstova, T.V.; Soloveva, N.A.; et al. 2023. Proteomic approach to investigating expression, localization, and functions of the sowahd gene protein product during granulocytic differentiation. Meta-Analysis, Biochemistry (Mosc), 88(10), 1668-1682.  PMID: 38105032
Yeom, S.; Nam, D.; Bok, K.H.; et al. 2023. Synthesis of S-carbamidomethyl cysteine and its use for quantification of cysteinyl peptides by targeted proteomics. Anal Chem, 95(38), 14413-14420. PMID: 37707799
Soloveva, N.; Novikova, S.; Farafonova, T.; et al. 2023. Proteomic signature of extracellular vesicles associated with colorectal cancer. Molecules, 28(10), 4227-4243. PMID: 37241967
Yussif, B.M.; Checco, J.W. 2022. Evaluation of endogenous peptide stereochemistry using liquid chromatography-mass spectrometry-based spiking experiments. Methods Enzymol, 663, 205-234. PMID: 35168790
Chavez, J.D.; Keller, A.; Wippel, H.H.; et al. 2021. Multiplexed cross-linking with isobaric quantitative protein interaction reporter technology. Anal Chem, 93(50), 16759-16768.
PMID: 34882395
McKay, M.J.; Marr, K.A.; Price, J.R.; et al. 2021. Lipid-dependent titration of glutamic acid at a bilayer membrane interface. CS Omega, 6(12), 8488-8494. PMID: 33817510
Lu, B.L.; Loomes, K.M.; Hay, D.L.; et al. 2020. Synthesis of isotopically labelled αCGRP8-37 and its lipidated analogue. J Labelled Comp Radiopharm, in press.  
Lau, J.K.-C.; Lam, K.H.B.; Lai, C.-K.; et al. 2019. Imidazolone formation from pronated tetrapeptides: effects of replacing a glycine by an alanine or proline residue. Int J Mass Spec, 435, 69-77. 
Li, F.; Cui, L.; Yu, D.; et al. 2019. Exogenous glutathione improves intracellular glutathione synthesis via the γ-glutamyl cycle in bovine zygotes and cleavage embryos. J Cell Physiol, 234(5), 7384-7394. PMID: 30362550
Orti, V.; Mertens, B.; Vialaret, J.; et al. 2018. Data from a targeted proteomics approach to discover biomarkers in saliva for the clinical diagnosis of perioddontitis. Data Brief, 18, 294-299. PMID: 29900194       
Peng, X.; Xu, X.; Wang, Y.; et al. 2018. A-to-I RNA editing contributes to proteomic diversity in cancer. Cancer Cell, 33(5), 817-828. PMID: 29706454       
Mertens, B.; Orti, V.; Vialaret, J.; et al. 2018. Assessing a multiplex-targeted proteomics approach for the clinical diagnosis of periodontitis using saliva samples. Bioanalysis, 10(1), 35-45. PMID: 29243487       
LeBlanc, A.; Michaud, S.A.; Percy, A.J.; et al. 2017. Multiplexed MRM-based protein quantitation using two different stable isotope-labeled peptide isotopologues for calibration. J Proteome Res, 16(7), 2527-2536. PMID: 28516774       
Percy, A.J.; Hardie, D.B.; Jardim, A.; Elliott, M.H.; Zhang, S.; Mohammed, Y.; Borchers, C.H. 2016. Multiplexed panel of precisely quantified salivary proteins for biomarker assessment. Proteomics, 17(6). PMID: 27538354       
Delgado, D.A., Doherty, K.; Cheng, Q.; Kim, H.; Xu, D.; Dong, H.; Grewer, C.; Qiang, W. 2016. Distinct membrane disruption pathways are induced by 40-residue β-amyloid peptides. J Biol Chem, 29(23), 12233-12244. PMID: 27056326       
Wang, D.; Krilich, J.; Baudys, J.; Barr, J.R.; Kalb, S.R. 2015. Optimization of peptide substrates for botulinum neurotoxin E improves detection sensitivity in the Endopep-MS assay. Anal Biochem, 468, 15-22. PMID: 25232998       
Hamid, M.; Theo, K.; Bong, K. 2013. Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proc Natl Acad Sci U S A, 110(9), 3645-3650. PMID: 23388641   Karlsson, C.; Malmstrom, L.; Aebersold, R. 2012. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat Commun, 3, 1301. PMID: 23250431       
Chambers, A.G.; Percy, A.J.; Yang, J. 2013. Multiplexed quantitation of endogenous proteins in dried blood spots by multiple reaction monitoring-mass spectrometry. Mol Cell Proteomics, 12(3), 781-91. PMID: 23221968       
Altvater, M.; Yiming, C.; Melnik, A. 2012. Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export. Mol Syst Biol, 8, 628. PMID: 23212245       
McClatchy, D.B.; Liao, L.; Park, S.K.; Venable, J.D.; Yates, J.R. 2007. Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res, 17(9), 1378-1388. PMID: 17675365       
Venable, J.D.; Wohlschlegel, J.; McClatchy, D.B.; Park, S.K.; Yates, J.R. III. 2007. Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. Anal Chem, 79(8), 3056-3064. PMID: 17367114        
McClatchy, D.B.; Dong, M.Q.; Wu, C.C.; Venable, J.D.; Yates, J.R. III. 2007. 15N metabolic labeling of mammalian tissue with slow protein turnover. J Proteome Res, 6(5), 2005-2010. PMID: 17375949