ArticleProteomics2010
LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments.
Article in Proteomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- IQUP identifies quantitatively unreliable spectra with machine learning for isobaric labeling-based proteomics.Scientific reports · 2025Article
- Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter.Scientific reports · 2023Article
- Quantitative Proteomics Using Isobaric Labeling: A Practical Guide.Genomics, proteomics & bioinformatics · 2021Review
- Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage.Scientific reports · 2021Article
- Comparative Analysis of Proteomics and Transcriptomics during Fertility Transition in a Two-Line Hybrid Rice Line Wuxiang S.International journal of molecular sciences · 2019Article
- Salivary proteomics in bisphosphonate-related osteonecrosis of the jaw.Oral diseases · 2015Article
- Isobaric labeling-based relative quantification in shotgun proteomics.Journal of proteome research · 2014Review
- Article
- Defining, comparing, and improving iTRAQ quantification in mass spectrometry proteomics data.Molecular & cellular proteomics : MCP · 2013Article
- Protein carbonylation and adipocyte mitochondrial function.The Journal of biological chemistry · 2012Article
- Comparison of 4-plex to 8-plex iTRAQ quantitative measurements of proteins in human plasma samples.Journal of proteome research · 2012Article
- Discovery- and target-based protein quantification using iTRAQ and pulsed Q collision induced dissociation (PQD).Journal of proteomics · 2012Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Pulsed Q dissociation enables combining LTQ ion trap instruments with isobaric peptide tagging. Unfortunately, this combination lacks a technique which accurately reports protein abundance ratios and is implemented in a freely available, flexible software pipeline. We developed and implemented a technique assigning collective reporter ion intensity-based weights to each peptide abundance ratio and calculating a protein's weighted average abundance ratio and p-value. Using an iTRAQ-labeled standard mixture, we compared our technique's performance to the commercial software MASCOT, finding that it performed better than MASCOT's nonweighted averaging and median peptide ratio techniques, and equal to its weighted averaging technique. We also compared performance of the LTQ-Orbitrap plus our technique to 4800 MALDI TOF/TOF plus Protein Pilot, by analyzing an iTRAQ-labeled stem cell lysate. We found highly correlated protein abundance ratios, indicating that the LTQ-Orbitrap plus our technique yields results comparable to the current standard. We implemented our technique in a freely available, automated software pipeline, called LTQ-iQuant, which is mzXML-compatible; supports iTRAQ 4-plex and 8-plex LTQ data; and can be modified for and have weights trained to a user's LTQ and other isobaric peptide tagging methods. LTQ-iQuant should make LTQ instruments and isobaric peptide tagging accessible to more proteomic researchers.
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