Mass Spectrometry-Based Proteomic Profiling

Peptides were reconstituted with 0.1% FA and separated by a linear gradient of solvent B (0.1% FA in ACN) using an EASY-nLC (Thermo Fisher Scientific, San Jose, CA, USA). MS data were analyzed on a Q-Exactive hybrid quadrupole-Orbitrap mass spectrometry (Thermo Fisher Scientific). MS data were searched against the Uniprot Human database (June 2014, 313,072 entries) with the SEQUEST (version 27; Thermo Fisher Scientific) program by Sorcerer^™. Results were reported with a ProteinProphet probability ≥ 99% and a PeptideProphet probability ≥ 95%7 (link) and MS/MS data were validated with Scaffold v.4.6.2 (Proteome Software, Portland, OR, USA). Label-free quantification was accomplished using the R program (version 2.15; R Foundation for Statistical Computing, Vienna, Austria) based power law global error model software (Bioconductor Software Packages, version 3.9) with statistically significant values (P value < 0.005 and signal-to-noise ratio ≥ ± 2).8 (link)

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Kim S.M., Cho B.K., Kim B.J., Lee H.Y., Norwitz E.R., Kang M.J., Lee S.M., Park C.W., Jun J.K., Yi E.C, & Park J.S. (2020). The Amniotic Fluid Proteome Differs Significantly between Donor and Recipient Fetuses in Pregnancies Complicated by Twin-to-Twin Transfusion Syndrome. Journal of Korean Medical Science, 35(10), e73.

Publication 2020

EASY-nLC Q-Exactive hybrid quadrupole-Orbitrap mass spectrometry R program

Human Hybrid Mass spectrometry Ms ms Peptides Proteome Solvent

Corresponding Organization :

Other organizations : Seoul National University Hospital, Seoul Metropolitan Government, Seoul National University, Boramae Medical Center, Tufts University

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Variable analysis

independent variables

Solvent B (0.1% FA in ACN) using an EASY-nLC (Thermo Fisher Scientific, San Jose, CA, USA)

dependent variables

MS data were analyzed on a Q-Exactive hybrid quadrupole-Orbitrap mass spectrometry (Thermo Fisher Scientific)
MS data were searched against the Uniprot Human database (June 2014, 313,072 entries) with the SEQUEST (version 27; Thermo Fisher Scientific) program by Sorcerer™
Label-free quantification was accomplished using the R program (version 2.15; R Foundation for Statistical Computing, Vienna, Austria) based power law global error model software (Bioconductor Software Packages, version 3.9)

control variables

Peptides were reconstituted with 0.1% FA

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