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Dataset Identifier

Metadata
datasetIdentifierPASS00390
datasetTypeSRM
submitterLik Wee Lee <llee@indidx.com>
submitter_organizationIntegrated Diagnostics
lab_head_full_namePaul Kearney
lab_head_emailpkearney@indidx.com
lab_head_organizationIntegrated Diagnostics
lab_head_countryUnited States
datasetTagIntegratedQuan
datasetTitleIntegrated Quantification method for precise and robust protein measurement in clinical proteomics
publicReleaseDate2014-12-25 00:00:00
finalizedDate2014-12-26 15:05:25
summaryBackground: Current quantification methods for mass spectrometry (MS)-based proteomics either do not provide sufficient control of variability or are difficult to implement for routine clinical testing.
Results: We present here an integrated quantification (InteQuan) method that better controls pre-analytical and analytical variability than the popular quantification method using stable isotope-labeled standard peptides (SISQuan). We quantified 16 lung cancer biomarker candidates in human plasma samples in three assessment studies, using immunoaffinity depletion coupled with multiple reaction monitoring (MRM) MS. InteQuan outperformed SISQuan in precision in all three studies and tolerated a two-fold difference in sample loading. The three studies lasted over six months and encountered major changes in experimental settings. Nevertheless, plasma proteins in low ng/ml to low μg/ml concentrations were measured with a median technical coefficient of variation (CV) of 11.9% using InteQuan. The corresponding median CV using SISQuan was 15.3% after linear fitting. Furthermore, InteQuan surpassed SISQuan in measuring biological difference among clinical samples and in distinguishing benign versus cancer plasma samples.
Conclusions: We demonstrated that InteQuan is a simple yet robust quantification method for MS-based quantitative proteomics, especially for applications in biomarker research and in routine clinical testing.
contributorsXiao-jun Li, Lik Wee Lee, Clive Hayward, Mi-Youn Brusniak, Pui-Yee Fong, Matthew McLean, JoAnne Mulligan, Douglas Spicer, Kenneth C. Fang, Stephen W. Hunsucker, Paul Kearney.
publicationAn integrated quantification method to increase the precision, robustness, and resolution of protein measurement in human plasma samples, Clinical Proteomics, Accepted.
growth
treatment
extraction
separationImmunoaffinity depletion with IgY14-Supermix resin columns (Sigma)
digestion
acquisition
informatics
instrumentsAgilent 6490 QQQ
speciesHuman
massModificationsnone

Official URL for this dataset: http://www.peptideatlas.org/PASS/PASS00390
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Servername: ftp.peptideatlas.org
Username: PASS00390
Password: HA2448v

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Listing of files:

 1.8K Jan 13  2014 PASS00390_DESCRIPTION-2014-00-13_092643.txt
 1.9K Dec 26  2014 PASS00390_DESCRIPTION-2014-11-26_145653.txt
 2.2K Dec 26  2014 PASS00390_DESCRIPTION.txt
  23M Jan 13  2014 Study_III_dataset.zip
  33M Jan 13  2014 Study_II_dataset.zip
  34M Jan 13  2014 Study_I_dataset.zip
  27K Jan 13  2014 transitions_SRMAtlas_format_20131113.csv

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