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Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.

Rudnick PA, Clauser KR, Kilpatrick LE, et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics. 2010;9(2):225-41. doi:10.1074/mcp.M900223-MCP200

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

Paulovich AG, Billheimer D, Ham AJL, et al. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol Cell Proteomics. 2010;9(2):242-54. doi:10.1074/mcp.M900222-MCP200

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.

Tabb DL, Vega-Montoto L, Rudnick PA, et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res. 2010;9(2):761-76. doi:10.1021/pr9006365

Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis.

Frühwirth R, Mani DR, Pyne S. Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis. BMC Bioinformatics. 2011;12:358. doi:10.1186/1471-2105-12-358

Optimizing performance of glycopeptide capture for plasma proteomics.

Berven FS, Ahmad R, Clauser KR, Carr SA. Optimizing performance of glycopeptide capture for plasma proteomics. J Proteome Res. 2010;9(4):1706-15. doi:10.1021/pr900845m

Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.

Udeshi ND, Svinkina T, Mertins P, et al. Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments. Mol Cell Proteomics. 2013;12(3):825-31. doi:10.1074/mcp.O112.027094

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

Abbatiello SE, Mani DR, Schilling B, et al. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics. 2013;12(9):2623-39. doi:10.1074/mcp.M112.027078

Identification of Trypanosome proteins in plasma from African sleeping sickness patients infected with T. b. rhodesiense.

Eyford BA, Ahmad R, Enyaru JC, Carr SA, Pearson TW. Identification of Trypanosome proteins in plasma from African sleeping sickness patients infected with T. b. rhodesiense. PLoS One. 2013;8(8):e71463. doi:10.1371/journal.pone.0071463

Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry.

Burgess MW, Keshishian H, Mani DR, Gillette MA, Carr SA. Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry. Mol Cell Proteomics. 2014;13(4):1137-49. doi:10.1074/mcp.M113.034660

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.

Lassen KG, Kuballa P, Conway KL, et al. Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proc Natl Acad Sci U S A. 2014;111(21):7741-6. doi:10.1073/pnas.1407001111