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GNPS - SiTrap proteomics profiling of renal normal/tumor tissue pairs

ABSTRACT: These are supporting RAW files for 'Detergent-free simultaneous sample preparation method for proteomics and metabolomics' SiTrap method manuscript. Frozen renal tissue from three matched clear cell renal carcinoma (G2 pT3a, G2 pT1b, G1 pT2) /adjacent normal sample pairs were obtained from The Leeds Multidisciplinary Research Tissue Bank. Approximately 1 cm2 sections with a thickness of 10 um were lysed and processed according to SiTrap protocol using SiTrap cellulose tips. The SiTrap load was normalized by protein concentration. 50 ug of protein was loaded. The collected flow-through fraction, devoid of proteins, was dried down for targeted metabolomics analysis. The captured protein fraction was reduced and alkylated in situ and digested with trypsin according to SiTrap protocol. The resulting peptides were concentrated for proteomics analysis.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Alexandre Zougman

PROVIDER: MSV000084405 | GNPS | Wed Oct 02 03:50:00 BST 2019

SECONDARY ACCESSION(S): PXD015677

REPOSITORIES: GNPS

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Project description:Recently, significant progress has been made in characterizing and sequencing the genomic alterations in statistically robust numbers of samples from several types of cancer. For example, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and other similar efforts are identifying genomic alterations associated with specific cancers (e.g., copy number aberrations, rearrangements, point mutations, epigenomic changes, etc.). The availability of these multi-dimensional data to the scientific community sets the stage for the development of new molecularly targeted cancer interventions. Understanding the comprehensive functional changes in cancer proteomes arising from genomic alterations and other factors is the next logical step in the development of high-value candidate protein biomarkers. Hence, proteomics can greatly advance the understanding of molecular mechanisms of disease pathology via the analysis of changes in protein expression, their modifications and variations, as well as protein-protein interaction, signaling pathways and networks responsible for cellular functions such as apoptosis and oncogenesis. Realizing this great potential, the NCI launched the second phase of the CPTC initiative in September 2011. Renamed the Clinical Proteomic Tumor Analysis Consortium, CPTAC is beginning to leverage its analytical outputs from Phase I to define cancer proteomes on genomically-characterized biospecimens. The purpose of this integrative approach is to provide the broad scientific community with knowledge that links genotype to proteotype and ultimately phenotype. The data contained in this dataset are derived from samples designed to confirm CPTAC findings from the TCGA samples. These confirmatory samples contain breast, ovarian, colon, and lung tumors collected via a protocol optimized for proteomics. Specifically, ischemic time of the sample was controlled and restricted to less than 30 minutes. ACGT, Inc. produced whole exome, mRNAseq, and miRNAseq for these samples. Corresponding proteomic data are available at: <a href="https://cptac-data-portal.georgetown.edu/cptacPublic/">https://cptac-data-portal.georgetown.edu/cptacPublic/</a> The study design was to profile colon, breast, ovarian, and lung tumors both genomically and proteomically. Germline DNA was obtained from blood. Normal control samples for proteomics varied by organ site: adjacent colon tissue for colon cases, contralateral breast tissue for some breast cases, and Fallopian tube fimbria for some ovarian cases. Lung cases had no normal control for proteomic analysis. All cancer samples were derived from primary and untreated tumors.

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GNPS - SiTrap proteomics profiling of renal normal/tumor tissue pairs

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