1,210
Views
6
CrossRef citations to date
0
Altmetric
Analytical Chemistry

Definitive screening design enables optimization of LC–ESI–MS/MS parameters in proteomics

, , &
Pages 2237-2243 | Received 18 Aug 2017, Accepted 04 Oct 2017, Published online: 25 Oct 2017

References

  • Beck M, Schmidt A, Malmstroem J, et al. The quantitative proteome of a human cell line. Mol Sys Biol. 2011;7(1):549.
  • Nagaraj N, Wisniewski JR, Geiger T, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Sys Biol. 2010;7:548–548.
  • Taniguchi Y, Choi PJ, Li G-W, et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010;329(5991):533–538.10.1126/science.1188308
  • Geiger T, Wehner A, Schaab C, et al. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics. 2012;11(3): M111-014050.
  • Michalski A, Cox J, Mann M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC−MS/MS. J Proteome Res. 2011;10(4):1785–1793.10.1021/pr101060v
  • Andrews GL, Dean RA, Hawkridge AM, et al. Improving proteome coverage on a LTQ-orbitrap using design of experiments. J Am Soc Mass Spectrom. 2011;22(4):773–783.10.1007/s13361-011-0075-2
  • Vollmer M, Hörth P, Nägele E. Optimization of two-dimensional off-line LC/MS separations to improve resolution of complex proteomic samples. Anal Chem. 2004;76(17):5180–5185.10.1021/ac040022u
  • Kalli A, Hess S. Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ-orbitrap mass analyzer. Proteomics. 2012;12(1):21–31.10.1002/pmic.v12.1
  • Xu P, Duong DM, Peng J. Systematical optimization of reverse-phase chromatography for shotgun proteomics. J Proteome Res. 2009;8(8):3944–3950.10.1021/pr900251d
  • Jones B, Nachtsheim CJ. A class of three-level designs for definitive screening in the presence of second-order effects. J Qual Technol. 2011;43(1):1.
  • Aburaya S, Esaka K, Morisaka H, et al. Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis. AMB Express. 2015;5(1):67.10.1186/s13568-015-0115-6
  • Morisaka H, Matsui K, Tatsukami Y, et al. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources. AMB Express. 2012;2(1):37.10.1186/2191-0855-2-37
  • Yamana R, Iwasaki M, Wakabayashi M, et al. Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot nano LC–MS/MS analysis with meter-scale monolithic silica columns. J Proteome Res. 2013;12(1):214–221.10.1021/pr300837u
  • Lemeer S, Hahne H, Pachl F, et al. Software tools for MS-based quantitative proteomics: a brief overview. In: Marcus K, editor. Quantitative methods in proteomics. Totowa, NJ: Humana Press; 2012. p. 489–499.10.1007/978-1-61779-885-6
  • Silva JC, Gorenstein MV, Li GZ, et al. Absolute quantification of proteins by LCMS(E) a virtue of parallel MS acquisition. Mol Cell Proteomics. 2006;5(1):144–156.10.1074/mcp.M500230-MCP200
  • Kalli A, Smith GT, Sweredoski MJ, et al. Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-orbitrap mass analyzers. J Proteome Res. 2013;12(7):3071–3086.10.1021/pr3011588
  • Hurvich CM, Tsai CL. Regression and time series model selection in small samples. Biometrika. 1989;76:297–307.
  • Cox J, Hein MY, Luber CA, et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014;13(9):2513–2526.10.1074/mcp.M113.031591
  • Feltcher ME, Gunawardena HP, Zulauf KE, et al. Label-free quantitative proteomics reveals a role for the Mycobacterium tuberculosis SecA2 pathway in exporting solute binding proteins and Mce transporters to the cell wall. Mol Cell Proteomics. 2015;14(6):1501–1516.10.1074/mcp.M114.044685
  • Horie K, Sato Y, Kimura T, et al. Estimation and optimization of the peak capacity of one-dimensional gradient high performance liquid chromatography using a long monolithic silica capillary column. J Chromatogr A. 2012;1228:283–291.10.1016/j.chroma.2011.12.088
  • Köcher T, Swart R, Mechtler K. Ultra-high-pressure RPLC hyphenated to an LTQ-orbitrap velos reveals a linear relation between peak capacity and number of identified peptides. Anal Chem. 2011;83(7):2699–2704.10.1021/ac103243t
  • Horie K, Kamakura T, Ikegami T, et al. Hydrophilic interaction chromatography using a meter-scale monolithic silica capillary column for proteomics LC–MS. Anal Chem. 2014;86(8):3817–3824.10.1021/ac4038625
  • Kim MS, Kandasamy K, Chaerkady R. Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-orbitrap mass spectrometer. J Am Soc Mass Spectrom. 2010;21(9):1606–1611.10.1016/j.jasms.2010.04.011
  • Pirmoradian M, Budamgunta H, Chingin K, et al. Rapid and deep human proteome analysis by single-dimension shotgun proteomics. Mol Cell Proteomics. 2013;12(11):3330–3338.10.1074/mcp.O113.028787
  • Schmidt A, Karas M, Dülcks T. Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI? J Am Soc Mass Spectrom. 2003;14(5):492–500.10.1016/S1044-0305(03)00128-4
  • Meiring HD, der Heeft VE. Nanoscale LC–MS (n): technical design and applications to peptide and protein analysis. J Sep Sci. 2002;25(9):557–568.10.1002/(ISSN)1615-9314
  • Shishkova E, Hebert AS, Coon JJ. Now, more than ever, proteomics needs better chromatography. Cell Syst. 2016;3(4):321–324.10.1016/j.cels.2016.10.007

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.