CPTAC CCRCC Discovery Study - DIA Proteome
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Hui Zhang
PROVIDER: MSV000093041 | MassIVE | Wed Oct 04 16:00:00 BST 2023
REPOSITORIES: MassIVE
Publications
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.
Clark David J DJ Dhanasekaran Saravana M SM Petralia Francesca F Pan Jianbo J Song Xiaoyu X Hu Yingwei Y da Veiga Leprevost Felipe F Reva Boris B Lih Tung-Shing M TM Chang Hui-Yin HY Ma Weiping W Huang Chen C Ricketts Christopher J CJ Chen Lijun L Krek Azra A Li Yize Y Rykunov Dmitry D Li Qing Kay QK Chen Lin S LS Ozbek Umut U Vasaikar Suhas S Wu Yige Y Yoo Seungyeul S Chowdhury Shrabanti S Wyczalkowski Matthew A MA Ji Jiayi J Schnaubelt Michael M Kong Andy A Sethuraman Sunantha S Avtonomov Dmitry M DM Ao Minghui M Colaprico Antonio A Cao Song S Cho Kyung-Cho KC Kalayci Selim S Ma Shiyong S Liu Wenke W Ruggles Kelly K Calinawan Anna A Gümüş Zeynep H ZH Geiszler Daniel D Kawaler Emily E Teo Guo Ci GC Wen Bo B Zhang Yuping Y Keegan Sarah S Li Kai K Chen Feng F Edwards Nathan N Pierorazio Phillip M PM Chen Xi Steven XS Pavlovich Christian P CP Hakimi A Ari AA Brominski Gabriel G Hsieh James J JJ Antczak Andrzej A Omelchenko Tatiana T Lubinski Jan J Wiznerowicz Maciej M Linehan W Marston WM Kinsinger Christopher R CR Thiagarajan Mathangi M Boja Emily S ES Mesri Mehdi M Hiltke Tara T Robles Ana I AI Rodriguez Henry H Qian Jiang J Fenyö David D Zhang Bing B Ding Li L Schadt Eric E Chinnaiyan Arul M AM Zhang Zhen Z Omenn Gilbert S GS Cieslik Marcin M Chan Daniel W DW Nesvizhskii Alexey I AI Wang Pei P Zhang Hui H
Cell 20191001 4
To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genom ...[more]
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2018-11-05 | MSV000083107 | MassIVE
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2019-08-28 | MSV000084246 | MassIVE
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the French Ligue Nationale Contre le Cancer (<a href=\\ttp://cit.ligue-cancer.net/\\ target=\\_blank\\>http://cit.ligue-cancer.net</a>). Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKIs) is a challenge. Our aim was to identify molecular markers associated with outcome in m-ccRCC patients treated with sunitinib.\
2016-02-26 | E-MTAB-3274 | biostudies-arrayexpress
Project description:<a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome" target="_blank">Explore This Study at the NCI Proteomic Data Commons</a><p>The goal of the CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue is to analyze the proteomes of TCGA tumor samples that have been comprehensively characterized by molecular methods (<a href="http://www.ncbi.nlm.nih.gov/pubmed/22810696" target="_blank">Cancer Genome Atlas Network, Nature 2012</a>).</p><p>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 <a href="https://portal.gdc.cancer.gov/projects/TCGA-COAD" target="_blank">Colon Adenocarcinoma (COAD)</a> samples and 31 are from the <a href="https://portal.gdc.cancer.gov/projects/TCGA-READ" target="_blank">Rectum Adenocarcinoma (READ)</a> 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. This work was accomplished by the Proteome Characterization Center (PCC) at Vanderbilt University led by Dr. Daniel C. Liebler. Clinical data files contain both the human readable TCGA bar codes and the UUIDs for each sample.</p><p>Complete Data Analysis from Vanderbilt University as published in Nature (Zhang, B., et al., Nature (2014) doi:10.1038/nature13438 Published online) is available <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S022">here</a>.</p><p>Data available on this study page (peptide spectrum matches and protein reports) are from the CPTAC Common Data Analysis Pipeline.</p><p>COAD tumor sample genomic data can be downloaded from <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">here</a>.<br/>READ tumor sample genomic data can be downloaded from <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">here</a>.<br/><br/>Colon tissue samples (ascending and descending) were obtained from 30 patients. Each sample was analyzed with label free global proteomic profiling. These colon samples, while derived from colon cancer subjects, did not contain tumor. Samples were obtained from the <a href="http://www.vicc.org/jimayersinstitute" target="_blank">Jim Ayers Institute for Precancer Detection and Diagnosis.</a> Data sets below are labeled with the patient identification number and contain data for both ascending and descending tissue samples. Data from colon tumor samples are available in the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S016" target="_blank">TCGA Colorectal Cancer study</a>.</p><ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S016">https://cptac-data-portal.georgetown.edu/cptac/s/S016</a> and <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S019">https://cptac-data-portal.georgetown.edu/cptac/s/S019</a> on 06/23/16</li><li>Dataset source: <a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome">https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome</a></li></ul>
2016-06-23 | MSV000079852 | MassIVE
Project description:<a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Breast_Cancer_Proteome|TCGA_Breast_Cancer_Phosphoproteome" target="_blank">Explore This Study at the NCI Proteomic Data Commons</a><p>Global proteome and phosphoproteome data have been acquired for 105 TCGA breast cancer samples using iTRAQ (isobaric Tags for Relative and Absolute Quantification) protein quantification methods. Samples were selected from each of the 4 breast tumor subtypes (Luminal A, Luminal B, Basal-like, HER2-enriched) described in the publication, <a href="http://www.ncbi.nlm.nih.gov/pubmed/23000897" target="_blank">Comprehensive molecular portraits of human breast tumors (Cancer Genome Atlas Network, Nature 2012)</a>.</p><p>Three TCGA samples and 1 common internal reference control sample are included in each iTRAQ experiment, consisting of 25 proteome and 13 phosphoproteome files. The internal reference is comprised of a mixture of 40 TCGA samples (of the 105 breast cancer samples) with equal representation of the 4 breast subtypes. Three of the TCGA samples have been assayed in duplicate for quality control purposes.</p><p>05TCGA_AO-A12D-01A_AN-A04A-01A_BH-A0AV-01A_Proteome_BI iTRAQ proteome data were acquired twice, before (20130310) and after (20130416) maintenance of the Q Exactive MS system. The "20130416" dataset was used in the final publication (see <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S029" target="_blank">here</a>).</p><p>Global proteome and phosphoproteome data were acquired for three normal breast samples in Experiment 37. Samples "263d3f-I", "blcdb9-I", and "c4155b-C" are normal breast tissue samples that were measured in the iTRAQ-114, -115, and -116 channels, respectively. All normal samples were compared to the internal reference sample in the iTRAQ-117 channel (see CPTAC, TCGA Breast Cancer iTRAQ Sample Mapping file below).</p><p>Information on the complete TCGA Breast invasive carcinoma cohort (BRCA) can be found <a href="https://portal.gdc.cancer.gov/projects/TCGA-BRCA" target="_blank">here</a>.<br/>Genomic data for the 105 TCGA samples used in the CPTAC Proteome study can be downloaded from <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-BRCA%22%5D%7D%7D%5D%7D" target="_blank">here</a>.</p><ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S015">https://cptac-data-portal.georgetown.edu/cptac/s/S015</a> on 10/15/18</li><li>Dataset source: <a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Breast_Cancer_Proteome|TCGA_Breast_Cancer_Phosphoproteome" target="_blank">https://pdc.esacinc.com/pdc/browse/filters/study_name:...</a></li></ul>
2018-10-18 | MSV000083043 | MassIVE
Project description:<a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome" target="_blank">Explore This Study at the NCI Proteomic Data Commons</a><p><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13438.html" target="_blank">Zhang, B., et al., Nature (2014) doi:10.1038/nature13438 Published online</a></p><p>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 <a href="https://portal.gdc.cancer.gov/projects/TCGA-COAD" target="_blank">Colon Adenocarcinoma (COAD)</a> samples and 31 are from the <a href="https://portal.gdc.cancer.gov/projects/TCGA-READ" target="_blank">Rectum Adenocarcinoma (READ)</a> 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.</p><p>TCGA_VU_N95<br/>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.</p><p>TCGA_VU_N95_Custom<br/>The Custom assembly represents the same samples, the sequence database has been augmented with nonsynonymous sequence variants detected by TCGA.<br/></p><p>TCGA_VU_N95-Normal_VU_N60<br/>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.</p><p>TCGA_Colorectal_Cancer_proBAM_PSM_genome_mapping_files<br/>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.</p><p>COAD tumor sample genomic data can be downloaded from <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">here</a>.<br/>READ tumor sample genomic data can be downloaded from <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">here</a>.<br/></p><p>Normal colon epithelium sample mass spectrometry data can be downloaded from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S019" target="_blank">here</a>.<br/>Mass spectrometry data for comparison and reference (CompRef) sample standards run with this study can be downloaded from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S017" target="_blank">here</a>.<br/>Peptide-Spectrum-Matches and Protein Reports from the CPTAC Common Data Analysis Pipeline (CDAP) can be downloaded from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S016" target="_blank">here</a>.<br/>Network analysis of this study can be viewed at the NetGestalt CRC Portal <a href="http://www.netgestalt.org/index.html" target="_blank">here</a>.<br/><br/>This work was accomplished by the Proteome Characterization Center (PCC) at Vanderbilt University led by Dr. Daniel C. Liebler.</p><ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S022">https://cptac-data-portal.georgetown.edu/cptac/s/S022</a> on 08/26/19</li><li>Dataset source: <a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome" target="_blank">https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Colon_Cancer_Proteome</a></li></ul>
2019-08-26 | MSV000084238 | MassIVE
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2019-08-30 | MSV000084260 | MassIVE
Project description:<p>Comparison and Reference (CompRef) Samples, initially characterized in the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S010">System Suitability Study</a>, were analyzed along with the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S016">TCGA colorectal cancer tumor samples</a> and with the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S019">normal colon epithelium samples</a>. These interstitial CompRef experiments are global proteomic profiling of the P6 (luminal) and P5 (basal) human-in-mouse xenograft breast carcinoma pooled samples.</p><p>One CompRef sample was run after every 5 samples of TCGA colorectal cancer tumor tissue, alternating between the P6 and P5 CompRef samples to generate 20 total data sets (designated as 01CompRef_P6_VU through 20CompRef_P5_VU).</p><p>Twelve CompRef samples were run with the 30 normal colon epithelium samples to produce 12 data sets (designated as 21CompRef_P6_VU through 32CompRef_P5_VU).</p>These experiments were used to monitor the consistency of laboratory protocols and mass spectrometry instrument performance during the TCGA colorectal cancer analysis.<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S017" target="_blank">https://cptac-data-portal.georgetown.edu/cptac/s/S017</a> on 08/31/18</li></ul>
2018-08-31 | MSV000082875 | MassIVE
Project description:Comparison and Reference (CompRef) Samples, initially characterized in the <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S010" target="_blank">System Suitability Study</a>, were analyzed along with the TCGA Breast Cancer tumor samples. These 5 iTRAQ experiments include proteome and phosphoproteome interrogation of both the P5 (basal) and P6 (luminal) human-in-mouse xenograft breast carcinoma pooled samples. The CompRef experiments were intercalated between the TCGA Breast Cancer experiments to monitor the consistency of laboratory protocols and mass spectrometry instrument performance.<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/cptac/s/S018">https://cptac-data-portal.georgetown.edu/cptac/s/S018</a> on 08/25/19</li></ul>
2019-08-25 | MSV000084233 | MassIVE