﻿Dataset EV2. Mass-spectrometric identification and quantification as well as phosphosite annotation data for phosphopeptides captured from cell lines, patient tumor biopsies, or patient-derived xenograft tumor material.

Data are presented for:
Cell Lines pTyr: phosphotyrosine-based immunoprecipitation of phosphopeptides from lysates of cell lines K562, H2228, SK-Mel-28, HCC827-ER3, and HCC827 (parental line for HCC827-ER3). Per cell line, two bioreplicates were analyzed with two technical replicates (injections) per bioreplicate.
Tumor Biopsies pTyr: phosphotyrosine-based immunoprecipitation of phosphopeptides from lysates of tumor biopies of patient 23 and patient 24 before and after erlotinib treatment (PreTx and Tx, respectively).
PDX Tumors pTyr: phosphotyrosine-based immunoprecipitation of phosphopeptides from lysates of patient-derived xenograft (human-in-mouse) tumor material originating from two colorectal tumor models (CRC0177, CRC0254). As a control, a colorectal tumor cell line (HCT116) lysate was included.
PDX Tumors TiOx: TiO2-based capture of phosphopeptides from lysates of patient-derived xenograft (human-in-mouse) tumor material originating from two colorectal tumor models (CRC0177, CRC0254). Two replicates per model.

 "Phosphopeptides" sheets contain selected columns from the pertinent MaxQuant 'modificationSpecificPeptides.txt ' export file detailing MS-based identification and quantification of captured phosphorylated peptides. Raw intensities were median normalized, and MS/MS spectral counts were obtained by utilizing the MaxQuant 'evidence.txt' export file. 

 "Phosphosites" sheets contain selected columns from the pertinent MaxQuant 'Phospho (STY)Sites.txt' export file listing phosphosites harbored by the identified phosphopeptides, as inferred by MaxQuant on the basis of mass-spectrometric evidence.

 The "Phosphosite IDs" columns (lightgrey headers) in both types of tables provide the cross table identifiers in the "Phosphosites" tables that link phosphosites to phosphopeptides in the "Phosphopeptides" table for which they were inferred.
