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PK, performed protein LC-MS/MS sample preparation and analysis by Spectra Mill bioinformatics software.
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The Spectrum Mill system was used for peptides identification.
Peptide quantification and protein identification were performed with Spectrum Mill MS Proteomics Workbench (Agilent Technologies).
For the Spectrum Mill analysis, the raw data were processed by Spectrum Mill MS Proteomics Workbench (Rev A.03.02.060b).
Spectrum Mill MS proteomics workbench software (Rev A.03.02.060, Agilent Technologies) was used to process the MS spectra and identifications were accepted with at least two unique peptides and with a score of more than 13.
The spectra identified by Spectrum Mill to be phopshorylated were manually verified and reported.
Mass spectra were processed with Spectrum Mill MS Proteomics workbench software (Agilent).
Human RefSeq Build 26 (~30,000 protein entries) was used for data search in Spectrum Mill.
As for Sequest, the Spectrum Mill thresholds are charge state dependent.
Protein quantitation was carried out using Spectrum Mill and Mascot Distiller (Version 2.3.1.0).
Peptide identification was performed by Spectrum Mill MS Proteomics Workbench (Rev B.04.00.127; Agilent Technologies).
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