CPTAC Data Portal and Proteomics Data Commons

1. CPTAC Data Portal & Proteomic Data Commons
Imaging SIG
July 1, 2019
Ratna Rajesh Thangudu, Ph.D.

2. Outline
• CPTAC Data Coordinating Center
• Proteomic Data Commons

3. CPTAC Data Coordinating Center
CPTAC Public Portal (https://proteomics.cancer.gov/data-portal)
• A centralized repository for the public dissemination of CPTAC proteomic datasets
• Analyze all of the CPTAC data through a Common Data Analysis Pipeline (CDAP) for public release
• Enable high speed transfer through UDP technology (Aspera)
• Provide support to the user community
CPTAC Assay Portal (https://proteomics.cancer.gov/assay-portal)
• The CPTAC Assay Portal serves as a centralized public repository of "fit-for-purpose," multiplexed quantitative
mass spectrometry-based proteomic targeted assays.

4. CPTAC Public Data Portal
https://proteomics.cancer.gov/data-portal

5. CPTAC Public Data Portal

6. CPTAC Data Portal: Releases

7. CPTAC Data Portal: Releases

8. CPTAC Data Portal: Releases

9. CPTAC Data Portal: Releases

10. Outline
• CPTAC Data Coordinating Center
• Proteomic Data Commons

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Proteomics Data
Commons (PDC)

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Proteomics Data Commons: High Level Goals
 Unsilo mass spectrometry data. Bring data into a common location
that satisfy Findability, Accessibility, Interoperability and Reusability
 Move from a situation where people move data to local tools to where
people move their tools to the data.
 Shift from a ‘data graveyard model’ to a ‘data workspace model’
 Make it feasible for pipelines to be released with data during
publication to improve reproducibility
 Improve meta-data annotations. Ensure data is annotated well using
common vocabularies but that the process is non-onerous.

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https://pdc.esacinc.com
Proteomic Data Commons:
now available as beta program
 Open to all users, no login required
 Enabled deep linking to connect
from CPTAC data portal
 Released UCEC and CCRCC
datasets from CPTAC3 program.
 Preparing to accept data from
APOLLO, ICPC, etc

14. PDC: Cloud architecture

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PDC: Data Model & Dictionary
• cancer Data Standards Registry and Repository (caDSR)
• NCI Thesaurus (NCIt)
• PSI MS Controlled Vocabularies and data formats

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Proteomics Data Commons: Common Data Analysis Pipeline

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PDC: Browse Data
The data,
including protein
expression data,
can be browsed
interactively using
a series of filters
and accessed by
API.

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PDC: Gene Summary

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PDC: Proteogenomic Integration

20. PDC: Workspace
• Private user data
repository
• Data submission
portal
• Environment for
analysis workflows.

21. PDC: Interoperability with CRDC
Source: CRDC DCF
Cloud Resources
- SBG CGC
- Broad FireCloud
- ISB CGC
Provide ability to access and stream data from across the CRDC resources with a single sign-on

22. Proteogenomics Across the CRDC
Ruggles et al. 2017, MCP 16(6) 959-981
Run full proteogenomic
pipelines using data
stored in the Commons

23. Data subtype File type Access
MS spectra .raw, mzmL Open
Peptide-spectrum
match
raw PSM,
.mzIdentmL
Open
Protein report .tsv Open
Genome-derived
protein sequence
FASTA Controlled
PDC: Controlled Access Data
Upcoming feature

24. PDC: Application Programming Interface

25. Jupyter Notebook Example
Get the TMT ratio data
Get the clinical metadata

26. Summary
 The PDC is being developed as a resource for democratized proteomics
data (MS and harmonized processed data plus rich metadata)
 Current public datasets are from CPTAC, others to follow
 The first full-release product will have both a portal and workspace
 Tool integration is underway with the NCI Cloud Resource partners
 It is currently under active development, with limited features available
 Community feedback is being actively solicited – please send your
thoughts
nci.pdc.help@esacinc.com

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Feedback: nci.pdc.help@esacinc.com

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Acknowledgements
ESAC, Inc
 Rajesh Thangudu
 Anand Basu
 Michael Holck
 Deepak Singhal
 Karen Ketchum
 Lei Ma
 Maya Zuhl
 Yi Xin
 Padimini Chilappagari
 Ngoc Nguyen
University of Washington
 Michael MacCoss
Spectragen Informatics
 Paul Rudnick
Georgetwon University
 Nathan Edwards
NCI
▪ Chris Kinsinger
▪ Erika Kim
▪ Tara Hiltke
Scientific Advisory Committee
▪ Nuno Bandeira – UCSD
▪ Tony Blau - UW
▪ David Fenyo - NYU
▪ Brad Gibson - Amgen
▪ Jake Jaffe – Broad
▪ Mark Musen - Stanford
▪ Michael Noble – Broad
▪ Sam Payne - PNNL
▪ Adam Resnick - CHOP
▪ Dan Spellman - Merck
Feedback : nci.pdc.help@esacinc.com