In Skyline (version 3.7.0.11317) a new document was created with default settings, plus Oxidation (M), Acetyl (N-Term), Amonia Loss (K, N, Q, R), and Water Loss (D, E, S, T) modifications, precursor charge states 1-7 and fragment charge states 1-6, for fragment types y, b and precursor, the 6 most intense library fragment ions and chromatogram extraction was set to use 15 ppm mass tolerance applying to all centroided MS/MS spectra using the 19 variable window isolation schemed defined in the paper, with 1 m/z margins, spanning 400-1220 m/z and 10 minutes of predicted retention times using the iRT values found in the paper assay library. Quantification result is the same as in RMSV000000252.1.The differential abundance analysis was performed by MSstats (v3.16.2) R package: Top 3 features were used for this reanalysis. Details for data processing and statistical analysis are available in description.pdf.
**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/C5PB05]
[See
results attachment job
for details]
Keywords: MassIVE.quant reviewed - Platinum
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Experimental Design | |
Conditions:
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Biological Replicates:
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Technical Replicates:
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Identification Results | |
Proteins (Human, Remapped):
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Proteins (Reported):
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Peptides:
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Variant Peptides:
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PSMs:
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Quantification Results | |
Differential Proteins:
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Quantified Proteins:
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Browse Reanalysis Files | |
Browse Quantification Results | Browse Metadata |
FTP Download Link (click to copy):
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