The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies
Abstract The proximity extension assay (PEA) enables large-scale proteomic investigations across numerous proteins and samples. However, discrepancies between measurements, known as batch-effects, potentially skew downstream statistical analyses and increase the risks of false discoveries. While imp...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-024-84320-4 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841544659846823936 |
|---|---|
| author | H. M. Smits E. M. Delemarre A. Pandit A. H. Schoneveld B. Oldenburg F. van Wijk S. Nierkens J. Drylewicz |
| author_facet | H. M. Smits E. M. Delemarre A. Pandit A. H. Schoneveld B. Oldenburg F. van Wijk S. Nierkens J. Drylewicz |
| author_sort | H. M. Smits |
| collection | DOAJ |
| description | Abstract The proximity extension assay (PEA) enables large-scale proteomic investigations across numerous proteins and samples. However, discrepancies between measurements, known as batch-effects, potentially skew downstream statistical analyses and increase the risks of false discoveries. While implementing bridging controls (BCs) on each plate has been proposed to mitigate these effects, a clear method for utilizing this strategy remains elusive. Here, we characterized batch effects in PEA proteomics and identified three types: protein-specific, sample-specific, and plate-wide. We developed a robust regression-based method called BAMBOO (Batch Adjustments using Bridging cOntrOls) to correct them. Simulations comparing BAMBOO with established correction techniques (median centering, median of the difference (MOD), and ComBat) revealed that median centering and ComBat were significantly impacted by outliers within the BCs, whereas BAMBOO and MOD were more robust when no plate-wide effects were introduced. Optimal batch correction was achieved with 10–12 BCs. We validated the simulation results using experimental data and found that BAMBOO and MOD had a reduced incidence of false discoveries compared to alternative methods. Our findings emphasize the prevalence of batch effects in PEA proteomic studies and advocate for BAMBOO as a robust and effective tool to enhance the reliability of large-scale analyses in the proteomic field. |
| format | Article |
| id | doaj-art-4e78651358f7448fad9aaa7fc324d944 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-4e78651358f7448fad9aaa7fc324d9442025-01-12T12:23:07ZengNature PortfolioScientific Reports2045-23222025-01-0115111110.1038/s41598-024-84320-4The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studiesH. M. Smits0E. M. Delemarre1A. Pandit2A. H. Schoneveld3B. Oldenburg4F. van Wijk5S. Nierkens6J. Drylewicz7Center for Translational Immunology, University Medical Center UtrechtCenter for Translational Immunology, University Medical Center UtrechtCenter for Translational Immunology, University Medical Center UtrechtCentral Diagnostic Laboratory, University Medical Center UtrechtDepartment of Gastroenterology and Hepatology, University Medical Center UtrechtCenter for Translational Immunology, University Medical Center UtrechtCenter for Translational Immunology, University Medical Center UtrechtCenter for Translational Immunology, University Medical Center UtrechtAbstract The proximity extension assay (PEA) enables large-scale proteomic investigations across numerous proteins and samples. However, discrepancies between measurements, known as batch-effects, potentially skew downstream statistical analyses and increase the risks of false discoveries. While implementing bridging controls (BCs) on each plate has been proposed to mitigate these effects, a clear method for utilizing this strategy remains elusive. Here, we characterized batch effects in PEA proteomics and identified three types: protein-specific, sample-specific, and plate-wide. We developed a robust regression-based method called BAMBOO (Batch Adjustments using Bridging cOntrOls) to correct them. Simulations comparing BAMBOO with established correction techniques (median centering, median of the difference (MOD), and ComBat) revealed that median centering and ComBat were significantly impacted by outliers within the BCs, whereas BAMBOO and MOD were more robust when no plate-wide effects were introduced. Optimal batch correction was achieved with 10–12 BCs. We validated the simulation results using experimental data and found that BAMBOO and MOD had a reduced incidence of false discoveries compared to alternative methods. Our findings emphasize the prevalence of batch effects in PEA proteomic studies and advocate for BAMBOO as a robust and effective tool to enhance the reliability of large-scale analyses in the proteomic field.https://doi.org/10.1038/s41598-024-84320-4ProteomicsLarge proteomic studyBatch effectsBatch effects correctionBridging controls |
| spellingShingle | H. M. Smits E. M. Delemarre A. Pandit A. H. Schoneveld B. Oldenburg F. van Wijk S. Nierkens J. Drylewicz The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies Scientific Reports Proteomics Large proteomic study Batch effects Batch effects correction Bridging controls |
| title | The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies |
| title_full | The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies |
| title_fullStr | The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies |
| title_full_unstemmed | The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies |
| title_short | The BAMBOO method for correcting batch effects in high throughput proximity extension assays for proteomic studies |
| title_sort | bamboo method for correcting batch effects in high throughput proximity extension assays for proteomic studies |
| topic | Proteomics Large proteomic study Batch effects Batch effects correction Bridging controls |
| url | https://doi.org/10.1038/s41598-024-84320-4 |
| work_keys_str_mv | AT hmsmits thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT emdelemarre thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT apandit thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT ahschoneveld thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT boldenburg thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT fvanwijk thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT snierkens thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT jdrylewicz thebamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT hmsmits bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT emdelemarre bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT apandit bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT ahschoneveld bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT boldenburg bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT fvanwijk bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT snierkens bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies AT jdrylewicz bamboomethodforcorrectingbatcheffectsinhighthroughputproximityextensionassaysforproteomicstudies |