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. The differential abundance analysis was performed by MSstats (v3.13.5) R package. Details for next steps are available in description.pdf.
**Publication : Choi et al. (Under revision) MSstats increases the reproducibility of detecting differentially abundant proteins across tools that process raw mass spectra.
[doi:10.25345/C5MT6N]
[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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