Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio

Dammer, Eric B.; Seyfried, Nicholas T.; Johnson, Erik C.B.

doi:10.3389/fsysb.2023.1092341

Cited by 19 publications

(10 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Protein abundance values can be normalized by TAMPOR (Tunable Approach for Median Polish of Ratio-Biological Abundance Batch Effect Removal) correction of data (Dammer et al, 2023). TAMPOR correction is a sophisticated and innovative approach applied in proteomics data analysis to address issues related to data quality and accuracy.…”

Section: Results Normalization and Analysis With Tampor Correctionmentioning

confidence: 99%

See 1 more Smart Citation

Data‐Independent Acquisition and Label‐Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid

Makepeace,

Rookyard,

Das

et al. 2024

Current Protocols

View full text Add to dashboard Cite

This article presents a practical guide to mass spectrometry–based data‐independent acquisition and label‐free quantification for proteomics analysis applied to cerebrospinal fluid, offering a robust and scalable approach to probing the proteomic composition of the central nervous system. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Cerebrospinal fluid sample collection and preparation for mass spectrometry analysisBasic Protocol 2: Mass spectrometry sample analysis with data‐independent acquisitionSupport Protocol: Data‐dependent mass spectrometry and spectral library constructionBasic Protocol 3: Analysis of mass spectrometry data

show abstract

Section: Results Normalization and Analysis With Tampor Correctionmentioning

confidence: 99%

“…The PEAKS software package is used for analysis of MS data (Xin et al, 2022). Additionally, the TAMPOR algorithm is used for results normalization and analysis (Dammer et al, 2023).…”

Section: Analysis Of Mass Spectrometry Datamentioning

confidence: 99%

Data‐Independent Acquisition and Label‐Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid

Makepeace,

Rookyard,

Das

et al. 2024

Current Protocols

View full text Add to dashboard Cite

show abstract

“…In large-scale TMT-MS proteomics studies, batch effects are inevitable due to technical reasons, especially when processing large cohorts in multiple separate batches (33,34). To investigate variability and clustering patterns associated with batch effects among frontal cortex samples prior to normalization and batch correction, we employed Multidimensional scaling (MDS) plot.…”

Section: Results: 31 Proteomics Data Quality Control In Frontal and T...mentioning

confidence: 99%

Large-scale Deep Proteomic Analysis in Alzheimer’s Disease Brain Regions Across Race and Ethnicity

Seifar,

Fox,

Shantaraman

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Introduction Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, yet our comprehension predominantly relies on studies within the non-Hispanic White (NHW) population. Here we aimed to provide comprehensive insights into the proteomic landscape of AD across diverse racial and ethnic groups. Methods Dorsolateral prefrontal cortex (DLPFC) and superior temporal gyrus (STG) brain tissues were donated from multiple centers (Mayo Clinic, Emory University, Rush University, Mt. Sinai School of Medicine) and were harmonized through neuropathological evaluation, specifically adhering to the Braak staging and CERAD criteria. Among 1105 DLPFC tissue samples (998 unique individuals), 333 were from African American donors, 223 from Latino Americans, 529 from NHW donors, and the rest were from a mixed or unknown racial background. Among 280 STG tissue samples (244 unique individuals), 86 were African American, 76 Latino American, 116 NHW and the rest were mixed or unknown ethnicity. All tissues were uniformly homogenized and analyzed by tandem mass tag mass spectrometry (TMT-MS). Results As a Quality control (QC) measure, proteins with more than 50% missing values were removed and iterative principal component analysis was conducted to remove outliers within brain regions. After QC, 9,180 and 9,734 proteins remained in the DLPC and STG proteome, respectively, of which approximately 9,000 proteins were shared between regions. Protein levels of microtubule-associated protein tau (MAPT) and amyloid-precursor protein (APP) demonstrated AD-related elevations in DLPFC tissues with a strong association with CERAD and Braak across racial groups. APOE4 protein levels in brain were highly concordant with APOE genotype of the individuals. Discussion This comprehensive region resolved large-scale proteomic dataset provides a resource for the understanding of ethnoracial-specific protein differences in AD brain.

show abstract

“…Each plate included 79 study samples, 4 replicates of the study pool, 1 procedural blank, 4 commercial serum and 8 commercial EDTA plasma samples. These serve as quality control (QC) and reference samples to compare, cross-reference and join large studies (Dammer et al, 2023; Pino et al, 2018). Measurements were performed on tryptic digests that have been created from the plasma citrate samples.…”

Section: Resultsmentioning

confidence: 99%

Pervasive Influence of Hormonal Contraceptives on the Human Plasma Proteome in a Broad Population Study

Dordevic,

Dierks,

Hantikainen

et al. 2023

Preprint

View full text Add to dashboard Cite

Large-scale plasma proteomics in population studies offer new avenues to explore non-genetic associations, such as biomarkers for lifestyle and environmental exposure. Moreover, through longitudinal monitoring, they help in characterizing the onset and progression of diseases. Utilizing the SWATH DIA-MS-based proteomic approach with 5-minute chromatographic gradients, we examined the neat plasma proteome of 3,632 participants from the Cooperative Health Research in South Tyrol (CHRIS) study. We present precise protein quantities for 148 highly abundant plasma protein groups. Many of these proteins are challenging to quantify using affinity-based reagents. This set of highly abundant plasma proteins includes immunoglobulins, coagulation factors, metabolic proteins, and components of the innate immune system, such as the complement system. Our findings indicate that, beyond age and sex, the most significant biological variable affecting the plasma proteome was the use of hormonal contraceptives. The signature from this drug class was more pronounced compared to other common medications, which influenced only a subset of the measured proteins and exhibited smaller effect sizes. Notably, Angiotensinogen (AGT) levels were strongly influenced by contraceptive use, suggesting that AGT levels might serve as a potential biomarker for contraceptive usage. Due to its high prevalence, and apparently strong influence, this type of medication should be accounted for in any epidemiological or clinical study of the plasma proteome to avoid spurious findings.

show abstract

Batch correction and harmonization of –Omics datasets with a tunable median polish of ratio

Cited by 19 publications

References 31 publications

Data‐Independent Acquisition and Label‐Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid

Data‐Independent Acquisition and Label‐Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid

Large-scale Deep Proteomic Analysis in Alzheimer’s Disease Brain Regions Across Race and Ethnicity

Pervasive Influence of Hormonal Contraceptives on the Human Plasma Proteome in a Broad Population Study

Contact Info

Product

Resources

About