ArticleJournal of the American Society for Mass Spectrometry2009
Differential protein expression analysis using stable isotope labeling and PQD linear ion trap MS technology.
Article in Journal of the American Society for Mass Spectrometry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
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- Isobaric labeling-based relative quantification in shotgun proteomics.Journal of proteome research · 2014Review
- Differential analysis of N-glycoproteome between hepatocellular carcinoma and normal human liver tissues by combination of multiple protease digestion and solid phase based labeling.Clinical proteomics · 2014Article
- Effects of lycopene on protein expression in human primary prostatic epithelial cells.Cancer prevention research (Philadelphia, Pa.) · 2013Article
- Discovery- and target-based protein quantification using iTRAQ and pulsed Q collision induced dissociation (PQD).Journal of proteomics · 2012Article
- MALDI mass spectrometric imaging of cardiac tissue following myocardial infarction in a rat coronary artery ligation model.Analytical chemistry · 2012Article
- Identification of proteins and phosphoproteins using pulsed Q collision induced dissociation (PQD).Journal of the American Society for Mass Spectrometry · 2011Article
- Impact of peptide modifications on the isobaric tags for relative and absolute quantitation method accuracy.Analytical chemistry · 2011Article
- LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments.Proteomics · 2010Article
- Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation.Molecular & cellular proteomics : MCP · 2010Article
- Fast proteomic protocol for biomarker fingerprinting in cancerous cells.Journal of chromatography. A · 2010Article
- Isobaric labeling and tandem mass spectrometry: a novel approach for profiling and quantifying proteins differentially expressed in amniotic fluid in preterm labor with and without intra-amniotic infection/inflammation.The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians · 2010Article
- Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response.Molecular & cellular proteomics : MCP · 2010Article
- Quantitative plasma proteomic profiling identifies the vitamin E binding protein afamin as a potential pathogenic factor in SIV induced CNS disease.Journal of proteome research · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An isotope tags for relative and absolute quantitation (iTRAQ)-based reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) method was developed for differential protein expression profiling in complex cellular extracts. The estrogen positive MCF-7 cell line, cultured in the presence of 17beta-estradiol (E2) and tamoxifen (Tam), was used as a model system. MS analysis was performed with a linear trap quadrupole (LTQ) instrument operated by using pulsed Q dissociation (PQD) detection. Optimization experiments were conducted to maximize the iTRAQ labeling efficiency and the number of quantified proteins. MS data filtering criteria were chosen to result in a false positive identification rate of <4%. The reproducibility of protein identifications was approximately 60%-67% between duplicate, and approximately 50% among triplicate LC-MS/MS runs, respectively. The run-to-run reproducibility, in terms of relative standard deviations (RSD) of global mean iTRAQ ratios, was better than 10%. The quantitation accuracy improved with the number of peptides used for protein identification. From a total of 530 identified proteins (P < 0.001) in the E2/Tam treated MCF-7 cells, a list of 255 proteins (quantified by at least two peptides) was generated for differential expression analysis. A method was developed for the selection, normalization, and statistical evaluation of such datasets. An approximate approximately 2-fold change in protein expression levels was necessary for a protein to be selected as a biomarker candidate. According to this data processing strategy, approximately 16 proteins involved in biological processes such as apoptosis, RNA processing/metabolism, DNA replication/transcription/repair, cell proliferation and metastasis, were found to be up- or down-regulated.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.