ArticleMolecular & cellular proteomics : MCP2019
Multibatch TMT Reveals False Positives, Batch Effects and Missing Values.
Article in Molecular & cellular proteomics : MCP, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
127 citing papers in PubMed, 220 citations in OpenAlex.
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- Mass spectrometry proteomics for studying mitostasis.Protein science : a publication of the Protein Society · 2026Review
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- MtrAB activates ectoine production and triggers sporulation in response to osmotic stress inMicrobiology (Reading, England) · 2026Article
- LIN28A-Dependent Kinome and Phosphoproteome Reprogramming Promotes Imatinib Resistance.Molecular & cellular proteomics : MCP · 2026Article
- Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.Nature communications · 2026Article
- The conserved two-component systems CutRS and CssRS control the protein secretion stress response inmBio · 2026Article
- optTMT: optimizing any experimental design to minimize false positives caused by TMT reporter ion interference.Bioinformatics advances · 2026Article
- Covariate balanced allocation of samples to batches to mitigate the impacts of technical variability.Bioinformatics advances · 2026Article
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- Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions.Analytical chemistry · 2025Article
- PROTRIDER: protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder.Bioinformatics (Oxford, England) · 2025Article
- Proteomics Data Imputation With a Deep Model That Learns From Many Datasets.Molecular & cellular proteomics : MCP · 2025Article
- The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells.Communications biology · 2025Review
- Data Processing and Analysis in Positional Proteomics.Proteomics · 2025Review
67 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Multiplexing strategies for large-scale proteomic analyses have become increasingly prevalent, tandem mass tags (TMT) in particular. Here we used a large iPSC proteomic experiment with twenty-four 10-plex TMT batches to evaluate the effect of integrating multiple TMT batches within a single analysis. We identified a significant inflation rate of protein missing values as multiple batches are integrated and show that this pattern is aggravated at the peptide level. We also show that without normalization strategies to address the batch effects, the high precision of quantitation within a single multiplexed TMT batch is not reproduced when data from multiple TMT batches are integrated.Further, the incidence of false positives was studied by using Y chromosome peptides as an internal control. The iPSC lines quantified in this data set were derived from both male and female donors, hence the peptides mapped to the Y chromosome should be absent from female lines. Nonetheless, these Y chromosome-specific peptides were consistently detected in the female channels of all TMT batches. We then used the same Y chromosome specific peptides to quantify the level of ion coisolation as well as the effect of primary and secondary reporter ion interference. These results were used to propose solutions to mitigate the limitations of multi-batch TMT analyses. We confirm that including a common reference line in every batch increases precision by facilitating normalization across the batches and we propose experimental designs that minimize the effect of cross population reporter ion interference.
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What OpenQuestion holds
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.