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HUPO test samples - A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

ABSTRACT: Not available

INSTRUMENT(S): appsQTOF1, QTOF-Ultima, ThermoFinnigan LTQ, Thermo Scientific LTQ Orbitrap, Bruker Daltonics esquire, LTQ-FT, LTQ, ABI 4800 TOF TOF, LTQ XL linear ion trap, Thermo Scientific LTQ, QSTAR Elite, Bruker MicroTof, LTQ-Orbitrap, Thermo Scientific LTQ FT, QTof Premier, LCQ XP, Unknown Instrument Name, Qstar pulsar I

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: A BELL

LAB HEAD: A BELL

PROVIDER: PRD000069 | Pride | 2009-05-15

REPOSITORIES: Pride

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Publications

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.

Bell Alexander W AW Deutsch Eric W EW Au Catherine E CE Kearney Robert E RE Beavis Ron R Sechi Salvatore S Nilsson Tommy T Bergeron John J M JJ

Nature methods 20090601 6

We performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially ...[more]

PMID: 19448641

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A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.

Project description:We performed a test sample study to try to identify errors leading to irreproducibility, including incompleteness of peptide sampling, in liquid chromatography-mass spectrometry-based proteomics. We distributed an equimolar test sample, comprising 20 highly purified recombinant human proteins, to 27 laboratories. Each protein contained one or more unique tryptic peptides of 1,250 Da to test for ion selection and sampling in the mass spectrometer. Of the 27 labs, members of only 7 labs initially reported all 20 proteins correctly, and members of only 1 lab reported all tryptic peptides of 1,250 Da. Centralized analysis of the raw data, however, revealed that all 20 proteins and most of the 1,250 Da peptides had been detected in all 27 labs. Our centralized analysis determined missed identifications (false negatives), environmental contamination, database matching and curation of protein identifications as sources of problems. Improved search engines and databases are needed for mass spectrometry-based proteomics.

| S-EPMC2785450 | biostudies-literature

HUPO Liver Proteome Project - Consortium project HUPO

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Gene level expression profiling of colorectal cancer tissue samples (test sample series)

Project description:This series is part of a larger series (GSE24549) of colorectal cancer tissue samples analyzed for global gene expression. The expression measures were used to develope a gene signature for prediction of prognosis in stage II and III colorectal cancer.

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Exon level expression profiling of colorectal cancer tissue samples (test sample series).

Project description:Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series.

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HUPO Brain Proteome Project - Pilot study of the Human Proteome Organisation Brain Proteome Project: applying different 2-DE techniques to monitor proteomic changes during murine brain development

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A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy.

Project description:Characterization of the human blood plasma proteome is critical to the discovery of routinely useful clinical biomarkers. We used an accurate mass and time (AMT) tag strategy with high-resolution mass accuracy cLC-FT-ICR MS to perform a global proteomic analysis of pilot study samples as part of the HUPO Plasma Proteome Project. HUPO reference serum and citrated plasma samples from African Americans, Asian Americans, and Caucasian Americans were analyzed, in addition to a Pacific Northwest National Laboratory reference serum and plasma. The AMT tag strategy allowed us to leverage two previously published "shotgun" proteomics experiments to perform global analyses on these samples in triplicate in less than 4 days total analysis time. A total of 722 (22% with multiple peptide identifications) International Protein Index redundant proteins, or 377 protein families by ProteinProphet, were identified over the six individual HUPO serum and plasma samples. The samples yielded a similar number of identified redundant proteins in the plasma samples (average 446 +/- 23) as found in the serum samples (average 440 +/- 20). These proteins were identified by an average of 956 +/- 35 unique peptides in plasma and 930 +/- 11 unique peptides in serum. In addition to this high-throughput analysis, the AMT tag approach was used with a Z-score normalization to compare relative protein abundances. This analysis highlighted both known differences in serum and citrated plasma such as fibrinogens, and reproducible differences in peptide abundances from proteins such as soluble activin receptor-like kinase 7b and glycoprotein m6b. The AMT tag strategy not only improved our sample throughput but also provided a basis for estimated quantitation.

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Sample size recalculation based on the prevalence in a randomized test-treatment study.

Project description:BackgroundRandomized test-treatment studies aim to evaluate the clinical utility of diagnostic tests by providing evidence on their impact on patient health. However, the sample size calculation is affected by several factors involved in the test-treatment pathway, including the prevalence of the disease. Sample size planning is exposed to strong uncertainties in terms of the necessary assumptions, which have to be compensated for accordingly by adjusting prospectively determined study parameters during the course of the study.MethodAn adaptive design with a blinded sample size recalculation in a randomized test-treatment study based on the prevalence is proposed and evaluated by a simulation study. The results of the adaptive design are compared to those of the fixed design.ResultsThe adaptive design achieves the desired theoretical power, under the assumption that all other nuisance parameters have been specified correctly, while wrong assumptions regarding the prevalence may lead to an over- or underpowered study in the fixed design. The empirical type I error rate is sufficiently controlled in the adaptive design as well as in the fixed design.ConclusionThe consideration of a blinded recalculation of the sample size already during the planning of the study may be advisable in order to increase the possibility of success as well as an enhanced process of the study. However, the application of the method is subject to a number of limitations associated with the study design in terms of feasibility, sample sizes needed to be achieved, and fulfillment of necessary prerequisites.

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Project description:Test study for genome submission

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