Browse
Submit Data
Databases
API
Help

Dataset Information

468 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

IQUARI - Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI)

ABSTRACT: Study on the MS1 interference problem for reporter ion quantification using orthogonal proteomes: human and pyrococcus furiosus.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Pyrococcus Furiosus Homo Sapiens (human)

TISSUE(S): Blood Platelet, Platelet, Permanent Cell Line Cell, Whole Body, Hela Cell

SUBMITTER: Marc Vaudel

LAB HEAD: Marc Vaudel

PROVIDER: PXD000013 | Pride | 2012-08-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_27082.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_27082.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_27082.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_27083.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_27083.pride.mztab.gz	Mztab

Items per page:

1 - 5 of 56

Publications

Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI).

Vaudel Marc M Burkhart Julia M JM Radau Sonja S Zahedi René P RP Martens Lennart L Sickmann Albert A

Journal of proteome research 20120830 10

With the increasing popularity of comparative studies of complex proteomes, reporter ion-based quantification methods such as iTRAQ and TMT have become commonplace in biological studies. Their appeal derives from simple multiplexing and quantification of several samples at reasonable cost. This advantage yet comes with a known shortcoming: precursors of different species can interfere, thus reducing the quantification accuracy. Recently, two methods were brought to the community alleviating the ...[more]

PMID: 22874012

Similar Datasets

A causal model of ion interference enables assessment and correction of ratio compression in multiplex proteomics

Project description:We thoroughly characterize isobaric labeling (TMT)-associated reporter ion interference at the MS2 level using a defined two-proteome experimental system with known ground truth. We discover remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2-scans - a discrepancy that we find resolved by considering co-fragmentation of peptide ions hidden within the spectral “noise” of the MS1 isolation window. On this basis, we establish a comprehensive regression modeling strategy for predicting accurate, feature-wise estimates of reporter ion interference. Finally, we demonstrate the utility of accurate ion purity estimates for accurate fold change estimation and unbiased PTM site-to-protein normalization.

2023-12-19 | PXD040449 | Pride

Isobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification - mouse tissue dataset

Project description:Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here we applied two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs (IMBR) makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between LC-MS runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in quantifiable n-plexes MS/MS spectra that can be used for quantification. Second, we introduce a novel PSM-level normalization, applicable to data with and without common reference channel. It is a weighted median-based method, in which the weights reflect the number of ions that were used for fragmentation. This dataset is TMT 8-plex samples without any referene channels.

2020-06-22 | PXD019880 | Pride

Isobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification - Peli1 knock-out mice dataset

Project description:Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs (IMBR) makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between LC-MS runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in quantifiable n-plexesMS/MS spectra that can be used for quantification. Second, we introduce a novel PSM-level normalization, applicable to data with and without common reference channel. It is a weighted median-based method, in which the weights reflect the number of ions that were used for fragmentation. On a typical dataset, we observe complete removal of batch effects and dominance of the biological sample grouping after normalization. This dataset is one of the datasets used for the study. It is TMT 10-plex with a reference channel.

2020-06-22 | PXD019881 | Pride

Investigating Reporter Ion Signal Characteristics in Isobaric Mass Tag Proteome Quantification Experiments

Project description:In this study we sought to examine the characteristics of the reporter ion signal obtained using current generation OT-based MS hardware. We initially focus on re-analysis of a previous experiment where TMT was using in combination with OT-MS3 to study protein expression diversity between histotypes of ovarian carcinoma where the presence of a notch – a region with no reported values – was observed in the reporter ion signal distributions.

2017-04-26 | PXD005892 | Pride

Ratio accuracy evaluation and correction using tandem mass tags

Project description:The multiplexing capabilities of isobaric mass tag based protein quantification, such as Tandem Mass Tags (TMT) or Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) have dramatically increased the scope of Mass Spectrometry (MS) based proteomics studies. Not only does the technology allow for the simultaneous quantification of multiple samples in a single MS injection, but its seamless compatibility with extensive sample pre-fractionation methods allow for comprehensive study of complex proteomes. However, reporter ion based quantification has often been criticized for limited quantification accuracy due to interference from co-eluting peptides and peptide fragments. In this study, we investigate the extent of this problem and propose an effective and easy-to-implement remedy relying on spiking a 6-protein calibration mixture to the samples subject to relative quantification. Our ratio adjustment approach was evaluated on a large scale TMT 10-plex dataset derived from cancer cell lines with chromosome instability. Furthermore, we analyzed a complex 2-proteome artificial sample mixture and investigated the precision of TMT and precursor ion intensity based Label Free Quantification. Comparing the two methods we observed that the isobaric tag based quantification workflow, due to its superior precision, was able to confirm more and smaller protein abundance changes, at a fixed False Positive Rate.

2016-07-01 | PXD003346 | Pride

GNPS Mono-Colonized GF Reporter Mice

Project description:Mono-colonized GF reporter mice fecal metabolomics by LC-MS/MS

2021-08-31 | MSV000088040 | GNPS

Assessing the effect of SUPT4H1 RNAi on the transcription of a repeat-containing reporter construct

Project description:SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recent studies propose a selective role for SUPT4H1 in transcription of repeat-containing transcripts, the translated products of which are a hallmark of neurodegeneration in disorders such as Huntington’s Disease and C9orf72-amyotrophic lateral sclerosis. To investigate the potential of SUPT4H1 as a therapeutic target in repeat-associated neurodegeneration, we engineered a reporter containing 71 hexanucleotide repeats (HNRs) encoding for pDi-amino acid repeats (DARPs) fused to EGFP. To approximate endogenous expression levels, the reporter also incorporated human C9orf72 intronic DNA immediately 5' of the hexanucleotide repeats. The reporter construct was integrated into the genome of HEK293t cells. We assessed the effect of depleting SUPT4H1 by RNAi interference on the transcriptome as a whole and on the DARP-EGFP reporter.

2019-01-01 | GSE121757 | GEO

Extensive Peptide Fractionation and y1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry

Project description:Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from co-isolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection and post-MS computational interference correction. We pooled tandem mass tag (TMT) labeled E. coli peptides at 1 : 3 : 10 ratios, and added in ~20-fold more rat peptides as background, followed by the analysis of two dimensional liquid chromatography (LC)-MS/MS. The quantitative interference was systematic investigated and the interference in MS2 scans were estimated by the intensity of contaminated y1 product ions. An algorithm was thus developed to correct reporter ion ratios of tryptic peptides.

2022-02-28 | PXD005797 | Pride

Ratio accuracy evaluation and correction using tandem mass tags

2018-08-27 | MSV000082855 | MassIVE