DOI: 10.25345/c50w8h
title: MassIVE MSV000084238 - Proteogenomic characterization of human colon and rectal cancer
title: &lt;a href='https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome' target='_blank'&gt;Explore This Study at the NCI Proteomic Data Commons&lt;/a&gt;&lt;p&gt;&lt;a href='http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13438.html' target='_blank'&gt;Zhang, B., et al., Nature (2014) doi:10.1038/nature13438 Published online&lt;/a&gt;&lt;/p&gt;&lt;p&gt;Proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) were analyzed along with integrated proteogenomic analyses. Ninety-five TCGA tumor samples were used in this study from 90 patients, with 5 samples representing different portions from the same tumor. The samples originated from two TCGA cohorts: 64 are from &lt;a href='https://gdc-portal.nci.nih.gov/projects/TCGA-COAD' target='_blank'&gt;Colon Adenocarcinoma (COAD)&lt;/a&gt; samples and 31 are from the &lt;a href='https://gdc-portal.nci.nih.gov/projects/TCGA-READ' target='_blank'&gt;Rectum Adenocarcinoma (READ)&lt;/a&gt; collection. The primary data from the liquid chromatography-tandem mass spectrometry (LC-MS/MS) global proteomic profiling of each tumor sample is associated with a data set in the table below. Three protein assemblies are provided from different protein database searches.&lt;/p&gt;&lt;p&gt;TCGA_VU_N95&lt;BR&gt;This assembly reflects the 95 TCGA samples for 90 tumors, spanning three search engines (MS-GF+, MyriMatch, and Pepitome), employing a standard RefSeq database and NIST spectral library.&lt;/p&gt;&lt;p&gt;TCGA_VU_N95_Custom&lt;BR&gt;The Custom assembly represents the same samples, the sequence database has been augmented with nonsynonymous sequence variants detected by TCGA.&lt;br&gt;&lt;/p&gt;&lt;p&gt;TCGA_VU_N95-Normal_VU_N60&lt;BR&gt;The third assembly contains the searches of the 95 TCGA samples employed in the first assembly alongside the 60 normal colons analyzed by Vanderbilt University as a control, employing the same three search engines, a standard RefSeq database, and a NIST spectral library.&lt;/p&gt;&lt;p&gt;TCGA_Colorectal_Cancer_proBAM_PSM_genome_mapping_files&lt;br&gt;Peptide spectrum matches from the TCGA_VU_N95_Custom IDPicker3 protein assembly were converted to protein BAM (proBAM) format for visualization, available in the metadata folder below.&lt;/p&gt; &lt;p&gt; COAD tumor sample genomic data can be downloaded from &lt;a href="https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TCGA-COAD%22%5D%7D%7D%5D%7D" target="_blank"&gt;here&lt;/a&gt;. &lt;br&gt; READ tumor sample genomic data can be downloaded from &lt;a href="https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TCGA-READ%22%5D%7D%7D%5D%7D" target="_blank"&gt;here&lt;/a&gt;.&lt;br&gt; &lt;/p&gt; &lt;p&gt; Normal colon epithelium sample mass spectrometry data can be downloaded from &lt;a href="/cptac/s/S019" target="_blank"&gt;here&lt;/a&gt;. &lt;br&gt; Mass spectrometry data for comparison and reference (CompRef) sample standards run with this study can be downloaded from &lt;a href="/cptac/s/S017" target="_blank"&gt;here&lt;/a&gt;. &lt;br&gt; Peptide-Spectrum-Matches and Protein Reports from the CPTAC Common Data Analysis Pipeline (CDAP) can be downloaded from &lt;a href="/cptac/s/S016" target="_blank"&gt;here&lt;/a&gt;. &lt;br&gt; Network analysis of this study can be viewed at the NetGestalt CRC Portal &lt;a href="http://www.netgestalt.org/index.html" target="_blank"&gt;here&lt;/a&gt;. &lt;br&gt; &lt;br&gt; This work was accomplished by the Proteome Characterization Center (PCC) at Vanderbilt University led by Dr. Daniel C. Liebler. &lt;/p&gt; &lt;ul&gt;&lt;li&gt;Dataset imported into MassIVE from &lt;a href="https://cptac-data-portal.georgetown.edu/cptac/s/S022"&gt;https://cptac-data-portal.georgetown.edu/cptac/s/S022&lt;/a&gt; on 08/26/19&lt;/li&gt; &lt;li&gt;Dataset source: &lt;a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome" target="_blank"&gt;https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt;