MS/MS spectra searched using MaxQuant (v1.5.2.8) and Andromeda as search engine as described previously were imported as a spectral library with a score filter>0.8. Extracted ion chromatograms were generated by Skyline daily v3.4.9.9576 within 5 min of the library retention time using 3 isotopic peaks for all peptides corresponding to the spiked-in proteins and the E.coli proteins previously identified with MaxQuant. Only peptides with charge +2 and +3 were considered. Automatic peak picking was manually reviewed for the spiked-in proteins and refined with idotp > 0.75 for the E. coli proteome. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.1. Top 5 features were used for statistical analysis in MSstats R package for this reanalysis.
**Publication : Tsai TH, Choi M, Banfai B, Liu Y, MacLean BX, Dunkley T, Vitek O. (2020). Selection of features with consistent proles improves relative protein quantification in mass spectrometry experiments. Molecular & Cellular Proteomics. 2020 March 31, 19(6) 944-959, doi:10.1074/mcp.RA119.001792. PMID: 32234965.
[doi:10.25345/C5GF0B]
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results attachment job
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Keywords: MassIVE.quant reviewed - Platinum
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Quantification Results | |
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Browse Reanalysis Files | |
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