- Original Article
- Open Access
Comparison of methods to examine the endogenous peptides of fetal calf serum
Clinical Proteomicsvolume 2, pages67–89 (2006)
There is a great desire to relate the patterns of endogenous peptides in blood to human disease and drug response. The best practices for the preparation of blood fluids for analysis are not clear and also relatively few of the peptides in blood have been identified by tandem mass spectrometry. We compared a number of sample preparation methods to extract endogenous peptides including C18 reversed phase, precipitation, and ultrafiltration. We examined the results of these sample preparation methods by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and liquid chromatography-tandem mass spectrometry (MS/MS) using MALDI-TOF/TOF and electrospray ionization-ion trap. Peptides from solid-phase extraction with C18 in the range of hundreds of femtomoles per spot were detected from the equivalent of 1 μL of serum by MALDI-TOF. We observed endogenous serum peptides from fibrinogen α- and β-chain, complement C3, α-2-HS-glycoprotein, albumin, serine (or cysteine) proteinase inhibitor, factor VIII, plasminogen, immunoglobulin, and other abundant blood proteins. However, we also recorded significant MS/MS spectra from tumor necrosis factor-α-, major histocompatibility complex-, and angiotensin-related peptides, as well as peptides from collagens and other low-abundance proteins. Amino acid substitutions were detected and a phosphorylated peptide was also observed. This is the first time the endogenous peptides of fetal serum have been examined by MS and where peptides from low-abundance proteins, phosphopeptides, and amino acid substitutions were detected.
Oleschuk, R. D., McComb, M. E., Chow, A. et al. (2000) Characterization of plasma proteins adsorbed onto biomaterials. By MALDI-TOFMS. Biomaterials 21, 1701–1710.
Weinberger, S. R., Morris, T. S., and Pawlak, M. (2000) Recent trends in protein biochip technology. Pharmacogenomics 1, 395–416.
Tammen, H., Hess, R., Uckert, S., et al. (2002) Detection of low-molecular-mass plasma peptides in the cavernous and systemic blood of healthy men during penile flaccidity and rigidity—an experimental approach using the novel differential peptide display technology. Urology 59, 784–789.
Guo, J., Yang, E. C., Desouza, L., et al. (2005) A strategy for high-resolution protein identification in surface-enhanced laser desorption/ionization mass spectrometry: Calgranulin A and chaperonin 10 as protein markers for endometrial carcinoma. Proteomics 5, 1953–1966.
Ardekani, A. M., Liotta, L. A., and Petricoin, E. F., 3rd. (2002) Clinical potential of proteomics in the diagnosis of ovarian cancer. Expert Rev. Mol. Diagn. 2, 312–320.
Karsan, A., Eigl, B. J., Flibotte, S., et al. (2005) Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin. Chem. 51, 1525–1528.
Marshall, J., Kupchak, P., Zhu, W., et al. (2003) Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction. J. Proteome Res. 2, 361–372.
Marshall, J., Jankowski, A., Furesz, S. et al. (2004) Human serum proteins preseparated by electrophoresis or chromatography followed by tandem mass spectrometry. J. Proteome Res. 3, 364–382.
Koomen, J. M., Li, D., Xiao, L. C., et al. (2005) Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J. Proteome Res. 4, 972–981.
Chertov, O., Biragyn, A., Kwak, L. W., et al. (2004) Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry. Proteomics 4, 1195–1203.
Ricard-Blum, S. and Ruggiero, F. (2005) The collagen superfamily: from the extracellular matrix to the cell membrane. Pathol. Biol. 53, 430–442.
Eisenberg, P. R., Sherman, L. A., Schectman, K., Perez, J., Sobel, B. E., and Jaffe, A. S. (1985) Fibrinopeptide A: a marker of acute coronary thrombosis. Circulation 71, 912–918.
Michael, I. P., Sotiropoulou, G., Pampalakis, G., et al. (2005) Biochemical and enzymatic characterization of human kallikrein 5 (hK5), a novel serine protease potentially involved in cancer progression. J. Biol. Chem. 280, 14,628–14,635.
Orvisky, E., Drake, S. K., Martin, B. M., et al. (2006) Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with hepatocellular carcinoma. Proteomics 6, 2895–2902.
Theodorescu, D., Wittke, S., Ross, M. M., et al. (2006) Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol. 7, 230–240.
Richter, R., Schulz-Knappe, P., Schrader, M., et al. (1999) Composition of the peptide fraction in human blood plasma: database of circulating human peptides. J. Chromatogr. B Biomed. Sci. Appl. 726, 25–35.
Villanueva, J., Philip, J., Entenberg, D., et al. (2004) Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem. 76, 1560–1570.
Lowenthal, M. S., Mehta, A. I., Frogale, K., et al. (2005) Analysis of albumin-associated peptides and proteins from ovarian cancer patients. Clin. Chem. 51, 1933–1945.
Lopez, M. F., Mikulskis, A., Kuzdzal, S., et al. (2005) High-resolution serum proteomic profiling of Alzheimer disease samples reveals disease-specific, carrier-protein-bound mass signatures. Clin. Chem. 51, 1946–1954.
Tirumalai, R. S., Chan, K. C., Prieto, D. A., Issaq, H. J., Conrads, T. P., and Veenstra, T. D. (2003) Characterization of the low molecular weight human serum proteome. Mol. Cell Proteomics 2, 1096–1103.
Marshall, J., Jankowski, A., Furesz, S., et al. (2004) Human serum proteins preseparated by electrophoresis or chromatography followed by tandem mass spectrometry. J. Proteome Res. 3, 364–382.
Craig, R. and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466–1467.
Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551–3567.
Adkins, J. N., Varnum, S. M., Auberry, K. J., et al. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell Proteomics 1, 947–955.
Chan, K., Lucas, D. A., Hise, D., et al. (2004) Analysis of the human serum proteome. Clin. Proteomics 1, 101–225.
Shen, Y., Kim, J., Strittmatter, E. F., et al. (2005) Characterization of the human blood plasma proteome. Proteomics 5, 4034–4045.
Kapp, E. A., Schutz, F., Connolly, L. M., et al. (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 5, 3475–3490.
Villanueva, J., Shaffer, D. R., Philip, J., et al. (2006) Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest. 116, 271–284.
Liotta, L. A. and Petricoin, E. F. Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. J. Clin. Invest. 116, 26–30.
Weinberger, S. R., Boschetti, E., Santambien, P., and Brenac, V. (2002) Surface-enhanced laser desorption-ionization retentate chromatography mass spectrometry (SELDI-RC-MS): a new method for rapid development of process chromatography conditions. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 782, 307–316.
Omenn, G. S., States, D. J., Adamski, M., et al. (2005) Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5, 3226–3245.
States, D. J., Omenn, G. S., Blackwell, T. W., et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 24, 333–338.
Diamandis, E. P. (2003) Point: proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin. Chem. 49, 1272–1275.
Pieper, R., Gatlin, C. L., Makusky, A. J., et al. (2003) The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 3, 1345–1364.
Anderson, N. L. and Anderson, N. G. (2003) The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics 2, 50.
Sviridov, D., Meilinger, B., Drake, S. K., Hoehn, G. T., and Hortin, G. L. (2006) Coelution of other proteins with albumin during size-exclusion HPLC: implications for analysis of urinary albumin. Clin. Chem. 52, 389–397.
Hortin, G. L., Shen, R. F., Martin, B. M., and Remaley, A. T. (2006) Diverse range of small peptides associated with high-density lipoprotein. Biochem. Biophys. Res. Commun. 340, 909–915.
Verhaert, P., Uttenweiler-Joseph, S., de Vries, M., Loboda, A., Ens, W., and Standing, K. G. (2001) Matrix-assisted laser desorption/ionization quadrupole time-of-light mass spectrometry: an elegant tool for peptidomics. Proteomics 1, 118–131.
Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A. (2004) The need for guidelines in publication of peptide and protein identification data: working group on publication guidelines for peptide and protein identification data. Mol. Cell Proteomics 3, 531–533.
Corthals, G. L., Aebersold, R., and Goodlett, D. R. (2005) identification of phosphorylation sites using microimmobilized metal affinity chromatography. Methods Enzymol. 405, 66–81.
Barling, P. M., Palmer, D. J., and Christie, D. L. (1986) Preparation of desulphated bovine fibrinopeptide B and demonstration of its sulphation in vitro by an enzyme system from neuroblastoma-glioma hybrid cells. Int. J. Biochem. 18, 137–141.
Krajewski, T. and Blomback, B. (1968) The location of tyrosine-O-sulphate in fibrinopeptides. Acta. Chem. Scand. 22, 1339–1346.
Lucas, J. and Henschen, A. (1986) Identification and assay of phosphoserine and tyrosine-O-sulphate in fibrinopeptides by reversed-phase high-performance liquid chromatography. J. Chromatogr. 369, 357–364.
Maurer, M. C., Peng, J. L., An, S. S., Trosset, J. Y., Henschen-Edman, A., and Scheraga, H. A. (1998) Structural examination of the influence of phosphorylation on the binding of fibrinopeptide A to bovine thrombin. Biochemistry 37, 5888–5902.
Seydewitz, H. H., Matthias, F. R., Schondorf, T. H., and Witt, I. (1987) Increase in the degree of phosphorylation of circulating fibrinogen under thrombolytic therapy with urokinase. Thromb. Res. 46, 437–445.
Lee, Y. H., Kim, M. S., Choie, W. S., Min, H. K., and Lee, S. W. (2004) Highly informative proteome analysis by combining improved N-terminal sulfonation for de novo peptide sequencing and online capillary reverse-phase liquid chromatography/tandem mass spectrometry. Proteomics 4, 1684–1694.
Hunt, D. F., Shabanowitz, J., Yates, J. R., 3rd, Zhu, N. Z., Russell, D. H., and Castro, M. E. (1987) Tandem quadrupole Fourier-transform mass spectrometry of oligopeptides and small proteins. Proc. Natl. Acad. Sci. USA 84, 620–623.
Bergquist, J., Palmblad, M., Wetterhall, M., Hakansson, P., and Markides, K. E. (2002) Peptide mapping of proteins in human body fluids using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Mass Spectrom. Rev. 21, 2–15.
Ping, P., Vondriska, T. M., Creighton, C. J., et al. (2005) A functional annotation of subproteomes in human plasma. Proteomics 5, 3506–3519.
About this article
- Fetal calf serum
- liquid chromatography-electrospray ionization mass spectrometry
- matrix-assisted laser desorption/ionization time-of-flight
- ESI tandem mass spectrometry