Spectrum Mill - Process Report
Spectrum Mill
Protigy
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Process Report
Generate GCT format if data directory contains a
*sample-annotation.csv file
, tab delimited format otherwise.
Data Directories
(None Selected)
Processing Parameters
Project:
Generic
CPTAC2 TCGA
Matrisome
Matrisome ECM
GO categories present
Gencode-smORFs-nuORFs-PG
Gencode-smORFs-nuORFs
smORFs-nuORFs
SM report type:
Protein - Protein Comparison, all use shared
Protein - Protein Comparison SGT, top uses shared
Protein - Protein Comparison SGS, ignore shared
Protein - Var Mod Site Comparison
Protein - Peptide Comparison
Protein - Prot Genom Site Comparison All
Protein - Prot Genom Site Comparison Variants
Protein - Prot Genom Site Comparison Spliceforms
Parse Report
Reporter ion label type:
Plot Ratio Distributions
Max plots per row:
X axis range:
to
Normalize Reporter Ratios
Method:
Median
Median / MAD
Median / SD
Mean
Mean / SD
Mix Model 2
GCT file options :
Retain Species:
All
Human | smORF
Rat
Combine replicate columns & omit QC.fail
Apply prior factors (for subsets to use aggregate)
Plot Ratio Distributions 2
Max plots per row:
X axis range:
to
Results
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