9 research outputs found
Analysis of allele-specific imbalance in discovery, validation, and combined sample sets.
*<p><i>Risk Allele Lost</i> refers to relative loss of risk allele compared to non-risk allele. Number in parentheses indicates percentage of total heterozygous samples showing relative loss of risk allele.</p>†<p><i>Non-risk Allele Lost</i> refers to relative loss of non-risk allele compared to risk allele. Number in parentheses indicates percentage of total heterozygous samples showing relative loss of non-risk allele.</p>§<p>Total number of tumors with imbalance/total heterozygous samples (% of heterozygotes showing imbalance).</p>‡<p>Chi-squared statistical test, df = 1.</p>∞<p>Bonferroni correction for 16 multiple comparisons (original) or 3 multiple comparisons (validation, combined).</p
CRC risk-associated GWAS SNPs assessed for allele-specific imbalance in the present study.
*<p>Position by UCSC Genome Browser (Human Feb. 2009 GRCh37/hg19 Assembly).</p>†<p>MAF = Minor Allele Frequency, as listed on NCBI dbSNP.</p>§<p>Odds Ratio from first listed GWAS reference (95% confidence interval). NA = not available.</p>‡<p>P-value from first listed GWAS reference.</p>∞<p>SNP positions in modest linkage disequilibrium (D′ = 0.76, ref. 15).</p>#<p>SNP positions in modest linkage disequilibrium (D′ = 0.71, ref. 15).</p>▵<p>SNP positions in high linkage disequilibrium (D′ = 0.99, ref. 9).</p
Analysis of allele-specific imbalance in discovery sample set.
*<p><i>Risk Allele Lost</i> refers to relative loss of the risk allele compared to the non-risk allele. Number in parentheses indicates percentage of total heterozygous samples showing relative loss of risk allele.</p>†<p><i>Non-risk Allele Lost</i> refers to relative loss of the non-risk allele compared to the risk allele. Number in parentheses indicates percentage of total heterozygous samples showing relative loss of non-risk allele.</p>§<p>Total number of tumors with imbalance/total heterozygous samples (% of heterozygotes showing imbalance).</p>‡<p>Chi-squared statistical test, df = 1. Unadjusted for multiple comparisons.</p
Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers
Plasma
proteomic experiments performed rapidly and economically
using several of the latest high-resolution mass spectrometers were
compared. Four quantitative hyperfractionated plasma proteomics experiments
were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three
Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments.
Each experiment compared two iTRAQ isobaric-labeled immunodepleted
plasma proteomes, provided as 30 labeled peptide fractions, and 480
LC–MS/MS runs delivered >250 GB of data in 2 months. Several
analysis algorithms were compared. At 1% false discovery rate, the
relative comparative findings concluded that the Thermo Scientific
Q Exactive Mass Spectrometer resulted in the highest number of identified
proteins and unique sequences with iTRAQ quantitation. The confidence
of iTRAQ fold-change for each protein is dependent on the overall
ion statistics (Mascot Protein Score) attainable by each instrument.
The benchmarking also suggested how to further improve the mass spectrometry
parameters and HPLC conditions. Our findings highlight the special
challenges presented by the low abundance peptide ions of iTRAQ plasma
proteome because the dynamic range of plasma protein abundance is
uniquely high compared with cell lysates, necessitating high instrument
sensitivity
Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers
Plasma
proteomic experiments performed rapidly and economically
using several of the latest high-resolution mass spectrometers were
compared. Four quantitative hyperfractionated plasma proteomics experiments
were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three
Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments.
Each experiment compared two iTRAQ isobaric-labeled immunodepleted
plasma proteomes, provided as 30 labeled peptide fractions, and 480
LC–MS/MS runs delivered >250 GB of data in 2 months. Several
analysis algorithms were compared. At 1% false discovery rate, the
relative comparative findings concluded that the Thermo Scientific
Q Exactive Mass Spectrometer resulted in the highest number of identified
proteins and unique sequences with iTRAQ quantitation. The confidence
of iTRAQ fold-change for each protein is dependent on the overall
ion statistics (Mascot Protein Score) attainable by each instrument.
The benchmarking also suggested how to further improve the mass spectrometry
parameters and HPLC conditions. Our findings highlight the special
challenges presented by the low abundance peptide ions of iTRAQ plasma
proteome because the dynamic range of plasma protein abundance is
uniquely high compared with cell lysates, necessitating high instrument
sensitivity
Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers
Plasma
proteomic experiments performed rapidly and economically
using several of the latest high-resolution mass spectrometers were
compared. Four quantitative hyperfractionated plasma proteomics experiments
were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three
Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments.
Each experiment compared two iTRAQ isobaric-labeled immunodepleted
plasma proteomes, provided as 30 labeled peptide fractions, and 480
LC–MS/MS runs delivered >250 GB of data in 2 months. Several
analysis algorithms were compared. At 1% false discovery rate, the
relative comparative findings concluded that the Thermo Scientific
Q Exactive Mass Spectrometer resulted in the highest number of identified
proteins and unique sequences with iTRAQ quantitation. The confidence
of iTRAQ fold-change for each protein is dependent on the overall
ion statistics (Mascot Protein Score) attainable by each instrument.
The benchmarking also suggested how to further improve the mass spectrometry
parameters and HPLC conditions. Our findings highlight the special
challenges presented by the low abundance peptide ions of iTRAQ plasma
proteome because the dynamic range of plasma protein abundance is
uniquely high compared with cell lysates, necessitating high instrument
sensitivity
Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers
Plasma
proteomic experiments performed rapidly and economically
using several of the latest high-resolution mass spectrometers were
compared. Four quantitative hyperfractionated plasma proteomics experiments
were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three
Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments.
Each experiment compared two iTRAQ isobaric-labeled immunodepleted
plasma proteomes, provided as 30 labeled peptide fractions, and 480
LC–MS/MS runs delivered >250 GB of data in 2 months. Several
analysis algorithms were compared. At 1% false discovery rate, the
relative comparative findings concluded that the Thermo Scientific
Q Exactive Mass Spectrometer resulted in the highest number of identified
proteins and unique sequences with iTRAQ quantitation. The confidence
of iTRAQ fold-change for each protein is dependent on the overall
ion statistics (Mascot Protein Score) attainable by each instrument.
The benchmarking also suggested how to further improve the mass spectrometry
parameters and HPLC conditions. Our findings highlight the special
challenges presented by the low abundance peptide ions of iTRAQ plasma
proteome because the dynamic range of plasma protein abundance is
uniquely high compared with cell lysates, necessitating high instrument
sensitivity
Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers
Plasma
proteomic experiments performed rapidly and economically
using several of the latest high-resolution mass spectrometers were
compared. Four quantitative hyperfractionated plasma proteomics experiments
were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three
Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments.
Each experiment compared two iTRAQ isobaric-labeled immunodepleted
plasma proteomes, provided as 30 labeled peptide fractions, and 480
LC–MS/MS runs delivered >250 GB of data in 2 months. Several
analysis algorithms were compared. At 1% false discovery rate, the
relative comparative findings concluded that the Thermo Scientific
Q Exactive Mass Spectrometer resulted in the highest number of identified
proteins and unique sequences with iTRAQ quantitation. The confidence
of iTRAQ fold-change for each protein is dependent on the overall
ion statistics (Mascot Protein Score) attainable by each instrument.
The benchmarking also suggested how to further improve the mass spectrometry
parameters and HPLC conditions. Our findings highlight the special
challenges presented by the low abundance peptide ions of iTRAQ plasma
proteome because the dynamic range of plasma protein abundance is
uniquely high compared with cell lysates, necessitating high instrument
sensitivity