Abstract
The combination of mass and normalized elution time (NET) of a peptide identified by liquid chromatography-mass spectrometry (LC-MS) measurements can serve as a unique signature for that peptide. However, the specificity of an LC-MS measurement depends upon the complexity of the proteome (i.e., the number of possible peptides) and the accuracy of the LC-MS measurements. In this work, theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity. Accuracy of the LC-MS measurement of mass-NET pairs (on a 0 to 1.0 NET scale) was described by bivariate normal sampling distributions centered on the peptide signatures. Measurement accuracy (i.e., mass and NET standard deviations of ±0.1, 1, 5, and 10 ppm, and ±0.01 and 0.05, respectively) was varied to evaluate improvements in process quality. The spatially localized confidence score, a conditional probability of peptide uniqueness, formed the basis for the peptide identification. Application of this approach to organisms with comparatively small proteomes, such as Deinococcus radiodurans, shows that modest mass and elution time accuracies are generally adequate for confidently identifying most peptides. For more complex proteomes, more accurate measurements are required. However, the study suggests that the majority of proteins for even the human proteome should be identifiable with reasonable confidence by using LC-MS measurements with mass accuracies within ±1 ppm and high efficiency separations having elution time measurements within ±0.01 NET.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Eng, J. K.; McCormack, A. L.; Yates, J. R. An Approach to Correlate Tandem Mass-Spectral Data of Peptides with Amino Acid Sequences in a Protein Database. J. Am. Soc. Mass Spectrom. 1994, 5(11), 976–989.
Washburn, M. P.; Wolters, D.; Yates, J. R. III. Large-Scale Analysis of the Yeast Proteome by Multidimensional Protein Identification Technology. Nat. Biotechnol. 2001, 19(3), 242–247.
Brock, A.; Horn, D.; Peters, E.; Shaw, C.; Ericson, C.; Phung, Q.; Salomon, A. An Automated Matrix-Assisted Laser Desorption/Ionization Quadrupole Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for “Bottom-Up” Proteomics. Anal. Chem. 2003, 75(14), 3419–3428.
Masselon, C.; Anderson, G.; Harkewicz, R.; Bruce, J.; Pasa-Tolic, L.; Smith, R. Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures. Anal. Chem. 2000, 72(8), 1918–1924.
Jacobs, J.; Monroe, M.; Qin, W.; Shen, Y.; Anderson, G.; Smith, R. Ultra-Sensitive, High Throughput, and Quantitative Proteomics Measurements. Int. J. Mass Spectrom. 2005, 240(3), 195–212.
Fung, K.; Askovic, S.; Basile, F.; Duncan, M. A Simple and Inexpensive Approach to Interfacing High-Performance Liquid Chromatography and Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry. Proteomics 2004, 4(10), 3121–3127.
Liu, T.; Qian, W.; Strittmatter, E.; Camp, D.; Anderson, G.; Thrall, B.; Smith, R. High-Throughput Comparative Proteome Analysis Using a Quantitative Cysteinyl-Peptide Enrichment Technology. Anal. Chem. 2004, 76(18), 5345–5353.
Nakamura, T.; Dohmae, N.; Takio, K. Characterization of a Digested Protein Complex with Quantitative Aspects: An Approach Based on Accurate Mass Chromatographic Analysis with Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry. Proteomics 2004, 4(9), 2558–2566.
Conrads, T. P.; Anderson, G. A.; Veenstra, T. D.; Pasa-Tolic, L.; Smith, R. D. Utility of Accurate Mass Tags for Proteome-Wide Protein Identification. Anal. Chem. 2000, 72(14), 3349–3354.
Zubarev, R.; Hakansson, P.; Sundqvist, B. Accuracy Requirements for Peptide Characterization by Monoisotopic Molecular Mass Measurements. Anal. Chem. 1996, 68(22), 4060–4063.
Cargile, B.; Stephenson, J. An Alternative to Tandem Mass Spectrometry: Isoelectric Point and Accurate Mass for the Identification of Peptides. Anal. Chem. 2004, 76(2), 267–275.
Palmblad, M.; Ramstrom, M.; Bailey, C.; McCutchen-Maloney, S.; Bergquist, J.; Zeller, L. Protein Identification by Liquid Chromatography-Mass Spectrometry Using Retention Time Prediction. J. Chromatogr. B 2004, 803(1), 131–135.
Palmblad, M.; Ramstrom, M.; Markides, K.; Hakansson, P.; Bergquist, J. Prediction of Chromatographic Retention and Protein Identification in Liquid Chromatography/Mass Spectrometry. Anal. Chem. 2002, 74(22), 5826–5830.
Spengler, B. De Novo Sequencing, Peptide Composition Analysis, and Composition-Based Sequencing: A New Strategy Employing Accurate Mass Determination by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2004, 15(5), 703–714.
Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative Analysis of Complex Protein Mixtures Using Isotope-Coded Affinity Tags. Nat. Biotechnol. 1999, 17(10), 994–999.
Liu, T.; Qian, W. J.; Strittmatter, E. F.; Camp, D. G. II; Anderson, G. A.; Thrall, B. D.; Smith, R. D. High-Throughput Comparative Proteome Analysis Using a Quantitative Cysteinyl-Peptide Enrichment Technology. Anal. Chem. 2004, 76(18), 5345–5353.
Ihling, C., Sinz, A. Proteome Analysis of Escherichia coli Using High-Performance Liquid Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Proteomics, in press.
Adkins, J. N.; Varnum, S. M.; Auberry, K. J.; Moore, R. J.; Angell, N. H.; Smith, R. D.; Springer, D. L.; Pounds, J. G. Toward a Human Blood Serum Proteome: Analysis by Multidimensional Separation Coupled with Mass Spectrometry. Mol. Cell. Proteom. 2002, 1(12), 947–955.
Durr, E.; Yu, J.; Krasinska, K. M.; Carver, L. A.; Yates, J. R.; Testa, J. E.; Oh, P.; Schnitzer, J. E. Direct Proteomic Mapping of the Lung Microvascular Endothelial Cell Surface In Vivo and in Cell Culture. Nat. Biotechnol. 2004, 22(8), 985–992.
Graumann, J.; Dunipace, L. A.; Seol, J. H.; McDonald, W. H.; Yates, J. R., III; Wold, B. J.; Deshaies, R. J. Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast. Mol. Cell. Proteom. 2004, 3(3), 226–237.
Lipton, M. S.; Pasa-Tolic, L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daly, M. J.; Fredrickson, J.; Hixson, K. K.; Kostandarithes, H.; Masselon, C.; Markillie, L. M.; Moore, R. J.; Romine, M. F.; Shen, Y.; Stritmatter, E.; Tolic, N.; Udseth, H. R.; Venkateswaran, A.; Wong, K. K.; Zhao, R.; Smith, R. D. Global Analysis of the Deinococcus radiodurans Proteome by Using Accurate Mass Tags. Proc. Natl. Acad. Sci. U.S.A. 2002, 99(17), 11049–11054.
Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. J. Proteome Res. 2003, 2(1), 43–50.
Shen, Y.; Jacobs, J. M.; Camp, D. G., II; Fang, R.; Moore, R. J.; Smith, R. D.; Xiao, W.; Davis, R. W.; Tompkins, R. G. Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome. Anal. Chem 2004, 6(4), 1134–1144.
Shen, Y.; Tolic, N.; Masselon, C.; Pasa-Tolic, L.; Camp, D. II; Lipton, M.; Anderson, G.; Smith, R. Nanoscale Proteomics. Anal. Bioanal. Chem. 2004, 378(4), 1037–1045.
Mohan, D.; Pasa-Tolic, L.; Masselon, C.; Tolic, N.; Bogdanov, B.; Hixson, K.; Smith, R.; Lee, C. Integration of Electrokinetic-Based Multidimensional Separation/Concentration Platform with Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry for Proteome Analysis of Shewanella oneidensis. Anal. Chem. 2003, 75(17), 4432–4440.
Petritis, K.; Kangas, L. J.; Ferguson, P. L.; Anderson, G. A.; Pasa-Tolic, L.; Lipton, M. S.; Auberry, K. J.; Strittmatter, E. F.; Shen, Y.; Zhao, R.; Smith, R. D. Use of Artificial Neural Networks for the Accurate Prediction of Peptide Liquid Chromatography Elution Times in Proteome Analyses. Anal. Chem. 2003, 75(5), 1039–1048.
Petritis, K. K. L.; Yorn, B.; Strittmatter, E. F.; Camp, D. G. II; Lipton, M.; Xu, Y.; Smith, R. D. Improved Liquid Chromatography peptide Elution Time Prediction by Using Artificial Neural Networks for Improved Proteomics Analysis. Proceedings of the 52nd ASMS Symposium; Nashville, TN, May 2004.
Jacobs, J. M.; Mottaz, H. M.; Yu, L. R.; Anderson, D. J.; Moore, R. J.; Chen, W. N.; Auberry, K. J.; Strittmatter, E. F.; Monroe, M. E.; Thrall, B. D.; Camp, D. G., II; Smith, R. D. Multidimensional Proteome Analysis of Human Mammary Epithelial Cells. J. Proteome Res. 2004, 3(1), 68–75.
Liu, T.; Qian, W. J.; Chen, W. J.; Jacobs, J. M.; Moore, R. J.; Anderson, D. J.; Gritsenko, M. A.; Monroe, M. E.; Thrall, B. D.; Camp, D. G., II; Smith, R. D. Improved Proteome Coverage by Using High Efficiency Cysteinyl-Peptide Enrichment: The Human Mammary Epithelial Cell Proteome. Proteomics, in press.
Monroe, M. E. Protein Digestion Simulator. http://ncrr.pnl.gov/softwarehttp://ncrr.pnl.gov/software/ (v2.0.1846.26324, 01/20/05).
Anderson, K. K.; Monroe, M. E.; Daly, D. S. Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations. Proceedings of the International Conference METMBS; Las Vegas, NV, June, 2004, pp 151–156.
Groen, F.; Mosleh, A. Foundations of Probabilistic Inference with Uncertain Evidence. Int. J. Approx. Reason 2005, 39(1), 49–83.
Ducret, A.; Van Oostveen, I.; Eng, J. K.; Yates, J. R. III; Aebersold, R. High Throughput Protein Characterization by Automated Reverse-Phase Chromatography/Electrospray Tandem Mass Spectrometry. Protein Sci. 1998, 7(3), 706–719
Author information
Authors and Affiliations
Corresponding author
Additional information
Published online June 23, 2005
A.D. Norbeck and M.E. Monroe made equal contributions to this article.
Rights and permissions
About this article
Cite this article
Norbeck, A.D., Monroe, M.E., Adkins, J.N. et al. The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes. J Am Soc Mass Spectrom 16, 1239–1249 (2005). https://doi.org/10.1016/j.jasms.2005.05.009
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1016/j.jasms.2005.05.009