Topograph, a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements

Edward J Hsieh; Nicholas J Shulman; Dao-Fu Dai; Evelyn S Vincow; Pabalu P Karunadharma; Leo Pallanck; Peter S Rabinovitch; Michael J MacCoss

doi:10.1074/mcp.O112.017699

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Topograph, a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements

Journal article

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Topograph, a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements

Edward J Hsieh, Nicholas J Shulman, Dao-Fu Dai, Evelyn S Vincow, Pabalu P Karunadharma, Leo Pallanck, Peter S Rabinovitch and Michael J MacCoss

Molecular & cellular proteomics, Vol.11(11), pp.1468-1474

11/2012

DOI: 10.1074/mcp.O112.017699

PMCID: PMC3494182

PMID: 22865922

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Abstract

Defects in protein turnover have been implicated in a broad range of diseases, but current proteomics methods of measuring protein turnover are limited by the software tools available. Conventional methods require indirect approaches to differentiate newly synthesized protein when synthesized from partially labeled precursor pools. To address this, we have developed Topograph, a software platform which calculates the fraction of peptides that are from newly synthesized proteins and their turnover rates. A unique feature of Topograph is the ability to calculate amino acid precursor pool enrichment levels which allows for accurate calculations when the precursor pool is not fully labeled, and the approach used by Topograph is applicable regardless of the stable isotope label used. We validate the Topograph algorithms using data acquired from a mouse labeling experiment and demonstrate the influence that precursor pool corrections can have on protein turnover measurements.

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Details

Title: Subtitle: Topograph, a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements
Creators: Edward J Hsieh - From the ‡Departments of Genome Sciences
Nicholas J Shulman - From the ‡Departments of Genome Sciences
Dao-Fu Dai - §Pathology and
Evelyn S Vincow - ¶Neurobiology and Behavior Program, University of Washington, Seattle, Washington 98195
Pabalu P Karunadharma - §Pathology and
Leo Pallanck - From the ‡Departments of Genome Sciences
Peter S Rabinovitch - §Pathology and
Michael J MacCoss - From the ‡Departments of Genome Sciences
Resource Type: Journal article
Publication Details: Molecular & cellular proteomics, Vol.11(11), pp.1468-1474
DOI: 10.1074/mcp.O112.017699
PMID: 22865922
PMCID: PMC3494182
NLM abbreviation: Mol Cell Proteomics
ISSN: 1535-9476
eISSN: 1535-9484
Publisher: The American Society for Biochemistry and Molecular Biology
Grant note: R01 DK069386; R01 GM086394; RC1 AG035844; R01 HL101186; P01 AG001751 / National Institutes of Health
Alternative title: Topograph, a Software Platform for Global Protein Turnover
Language: English
Date published: 11/2012
Academic Unit: Pathology; Iowa Neuroscience Institute; Radiation Oncology
Record Identifier: 9984046813002771

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