Quantitative accuracy in mass spectrometry based proteomics of complex samples: The impact of labeling and precursor interference

Sandberg, AnnSofi; Branca, Rui M.; Lehtiö, Janne; Forshed, Jenny

doi:10.1016/j.jprot.2013.10.035

Cited by 82 publications

(83 citation statements)

References 42 publications

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“…Thus, we expect our calibration mix based ratio adjustment method to be more robust. The efficacy of the S2I ratio correction method is limited by the correlation between relative interference intensity within the precursor selection window and relative reporter ion interference intensity, which has been shown to be rather poor in some experiments 39 . Notably, we consistently see in our datasets that the S2I metric underestimates the TMT interference intensities.…”

Section: Discussionmentioning

confidence: 99%

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

et al. 2016

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The multiplexing capabilities of isobaric mass tag-based protein quantification, such as Tandem Mass Tags or Isobaric Tag for Relative and Absolute Quantitation have dramatically increased the scope of mass spectrometry-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 prefractionation methods allows for comprehensive studies of complex proteomes. However, reporter ion-based quantification has often been criticized for limited quantification accuracy due to interference from coeluting peptides and peptide fragments. In this study, we investigate the extent of this problem and propose an effective and easy-to-implement remedy that relies on spiking a 6-protein calibration mixture to the samples. We evaluated our ratio adjustment approach using two large scale TMT 10-plex data sets derived from a human cancer and noncancer cell line as well as E. coli cells grown at two different conditions. Furthermore, we analyzed a complex 2-proteome artificial sample mixture and investigated the precision of TMT and precursor ion intensity-based label free quantification. Studying the protein set identified by both methods, we found that differentially abundant proteins were assigned dramatically higher statistical significance when quantified using TMT. Data are available via ProteomeXchange with identifier PXD003346.

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Section: Discussionmentioning

confidence: 99%

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

et al. 2016

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“…Coefficient of variation (CV) values were the primary parameters used to validate the data. Proteins with variability in reporter ion signals above 30% were excluded from the analysis as described earlier37. Additionally, during statistical analyses all proteins were filtered and only hits present in at least 75% of samples were retained.…”

Section: Methodsmentioning

confidence: 99%

iTRAQ-based proteomic analysis of plasma reveals abnormalities in lipid metabolism proteins in chronic kidney disease-related atherosclerosis

Łuczak

Formanowicz

Marczak

et al. 2016

Sci Rep

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Patients with chronic kidney disease (CKD) have a considerably higher risk of death due to cardiovascular causes. Using an iTRAQ MS/MS approach, we investigated the alterations in plasma protein accumulation in patients with CKD and classical cardiovascular disease (CVD) without CKD. The proteomic analysis led to the identification of 130 differentially expressed proteins among CVD and CKD patients and healthy volunteers. Bioinformatics analysis revealed that 29 differentially expressed proteins were involved in lipid metabolism and atherosclerosis, 20 of which were apolipoproteins and constituents of high-density lipoprotein (HDL) and low-density lipoprotein (LDL). Although dyslipidemia is common in CKD patients, we found that significant changes in apolipoproteins were not strictly associated with changes in plasma lipid levels. A lack of correlation between apoB and LDL concentration and an inverse relationship of some proteins with the HDL level were revealed. An increased level of apolipoprotein AIV, adiponectin, or apolipoprotein C, despite their anti-atherogenic properties, was not associated with a decrease in cardiovascular event risk in CKD patients. The presence of the distinctive pattern of apolipoproteins demonstrated in this study may suggest that lipid abnormalities in CKD are characterized by more qualitative abnormalities and may be related to HDL function rather than HDL deficiency.

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“…To scan a comprehensive differential proteome for saccular intracranial aneurysms tissues, we used a 4-plex isobaric tag for isobaric tags for relative and absolute quantification (iTRAQ), allowing us to identify and quantify proteins in up to 4 samples [7]. Quantitative proteome is a powerful technology for large scare of differential proteins between different samples.…”

Section: Introductionmentioning

confidence: 99%

Comparative proteome analysis of saccular intracranial aneurysms with iTRAQ quantitative proteomics

Jia

Huang

et al. 2016

Journal of Proteomics

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Quantitative accuracy in mass spectrometry based proteomics of complex samples: The impact of labeling and precursor interference

Cited by 82 publications

References 42 publications

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

iTRAQ-based proteomic analysis of plasma reveals abnormalities in lipid metabolism proteins in chronic kidney disease-related atherosclerosis

Comparative proteome analysis of saccular intracranial aneurysms with iTRAQ quantitative proteomics

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