Evaluation of regular UPLC/MS system for experimental and clinical proteomics

Abstract

The objective of this study was to investigate if UPLC/MS system without chip or Jetstream technology could be used in proteomics. A regular UPLC column (2.1 mm × 150 mm, 1.7 μm) was used to separate peptides at a flow rate of 0.200 mL/min. First, bovine serum albumin samples were analyzed with intra- and inter-day (11 days) experiments. In Escherichia coli experiments, 518 proteins were identified and subsequently investigated with PANTHER gene list and KEGG pathway. Results demonstrated that UPLC/MS provides detailed information regarding cellular process. Finally, we analyzed human plasma sample to observe if UPLC/MS system could be used to analyze body fluids. We identified 87 proteins in the plasma sample, and the identified proteins were investigated in terms of molecular biology. The results showed that UPLC/MS system could provide promising results for experimental and clinical proteomics.

Keywords

• Chromatography
• maxquant
• proteomics
• E. coli
• plasma

References

1. [1] Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem. 2001; 70: 437-473. [CrossRef]
2. [2] Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature. 2003; 422(6928): 208-215. [CrossRef]
3. [3] Wright PC, Noirel J, Ow SY, Fazeli A. A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology. 2012; 77(4): 738-765. [CrossRef]
4. [4] Mann M. Origins of mass spectrometry-based proteomics. Nat Rev Mol Cell Biol. 2016; 17(11): 678-685. [CrossRef]
5. [5] Doerr A. Mass spectrometry-based targeted proteomics. Nat Methods. 2013; 10(1): 23. [CrossRef]
6. [6] Resing KA, Ahn NG. Proteomics strategies for protein identification. FEBS Lett. 2005; 579(4): 885-889. [CrossRef]
7. [7] Sidoli S, Lin S, Karch KR, Garcia BA. Bottom-Up and Middle-Down Proteomics Have Comparable Accuracies in Defining Histone Post-Translational Modification Relative Abundance and Stoichiometry. Anal Chem. 2015; 87(6): 3129-3133. [CrossRef]
8. [8] Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A. 2004; 101(37): 13417-13422. [CrossRef]

9. [9] Liu J, Bell A, Bergeron J, Yanofsky C, Carrillo B, Beaudrie C, Robert E. Methods for peptide identification by spectral comparison. Proteome SCI. 2007; 5. [CrossRef]
10. [10] Rabilloud T, Lelong C. Two-dimensional gel electrophoresis in proteomics: A tutorial. J proteomics. 2011; 74(10): 1829-1841. [CrossRef]
11. [11] Galeva N, Altermann M. Comparison of one-dimensional and two-dimensional gel electrophoresis as a separation tool for proteomic analysis of rat liver microsomes: Cytochromes P450 and other membrane proteins. Proteomics. 2002; 2(6): 713-722. [CrossRef]
12. [12] Chenau J, Michelland S, Sidibe J, Seve M. Peptides OFFGEL electrophoresis: a suitable pre-analytical step for complex eukaryotic samples fractionation compatible with quantitative iTRAQ labeling. Proteome SCI . 2008; 6(1): 1-8. [CrossRef]
13. [13] Fukao Y, Yoshida M, Kurata R, Kobayashi M, Nakanishi M, Fujiwara M. Peptide Separation Methodologies for InDepth Proteomics in Arabidopsis. Plant cell physiol. 2013; 54(5): 808-815. [CrossRef]
14. [14] Saz JM, Marina ML. Application of micro- and nano-HPLC to the determination and characterization of bioactive and biomarker peptides. J Sep Sci. 2008; 31(3): 446-458. [CrossRef]
15. [15] Wilson SR, Vehus T, Berg HS, Lundanes E. Nano-LC in proteomics: recent advances and approaches. Bioanalysis. 2015; 7(14): 1799-1815. [CrossRef]
16. [16] Waanders LF, Chwalek K, Monetti M, Kumar C, Lammert E, Mann M. Quantitative proteomic analysis of single pancreatic islets. Proc Natl Acad Sci USA. 2009; 106(45): 18902-18907. [CrossRef]
17. [17] Qian WJ, Jacobs JM, Liu T, Camp DG, Smith RD. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics. 2006; 5(10): 1727-1744. [CrossRef]
18. [18] Noga M, Sucharski F, Suder P, Silberring J. A practical guide to nano-LC troubleshooting. J Sep Sci. 2007; 30(14): 2179- 89. [CrossRef]
19. [19] Kocher T, Pichler P, Swart R, Mechtler K. Analysis of protein mixtures from whole-cell extracts by single-run nanoLCMS/MS using ultralong gradients. Nat Protoc. 2012; 7(5): 882-890. [CrossRef]
20. [20] Percy AJ, Chambers AG, Smith DS, Borchers CH. Standardized protocols for quality control of MRM-based plasma proteomic workflows. J Proteome Res. 2013; 12(1): 222-233. [CrossRef]
21. [21] Gonzalez Fernandez-Nino SM, Smith-Moritz AM, Chan LJ, Adams PD, Heazlewood JL, Petzold CJ. Standard flow liquid chromatography for shotgun proteomics in bioenergy research. Front Bioeng Biotechnol. 2015; 3: 44. [CrossRef]
22. [22] Krokhin OV. Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. Anal Chem. 2006; 78(22): 7785-7795. [CrossRef]
23. [23] Koçak E. PhD Thesis. Liquid Choromatography-Mass Spectroscopy Based Proteomics Studies on Caco-2 Colon cancer cells. Analytical Chemistry Department, Faculty of Pharmacy, Hacettepe University; 2017.