Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments

L Gatto, R Aebersold, J Cox, V Demichev, J Derks… - Nature …, 2023 - nature.com
Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently
become technically feasible. While such analysis has the potential to accurately quantify …

Dealing with missing values in proteomics data

W Kong, HWH Hui, H Peng, WWB Goh - Proteomics, 2022 - Wiley Online Library
Proteomics data are often plagued with missingness issues. These missing values (MVs)
threaten the integrity of subsequent statistical analyses by reduction of statistical power …

Revisiting the thorny issue of missing values in single-cell proteomics

C Vanderaa, L Gatto - Journal of Proteome Research, 2023 - ACS Publications
Missing values are a notable challenge when analyzing mass spectrometry-based
proteomics data. While the field is still actively debating the best practices, the challenge …

Evaluating proteomics imputation methods with improved criteria

L Harris, WE Fondrie, S Oh… - Journal of proteome …, 2023 - ACS Publications
Quantitative measurements produced by tandem mass spectrometry proteomics
experiments typically contain a large proportion of missing values. Missing values hinder …

BIRCH: an automated workflow for evaluation, correction, and visualization of batch effect in bottom-up mass spectrometry-based proteomics data

N Sundararaman, A Bhat, V Venkatraman… - Journal of proteome …, 2023 - ACS Publications
Recent surges in large-scale mass spectrometry (MS)-based proteomics studies demand a
concurrent rise in methods to facilitate reliable and reproducible data analysis …

ProJect: a powerful mixed-model missing value imputation method

W Kong, BJH Wong, HWH Hui, KP Lim… - Briefings in …, 2023 - academic.oup.com
Missing values (MVs) can adversely impact data analysis and machine-learning model
development. We propose a novel mixed-model method for missing value imputation (MVI) …

Comparative assessment and novel strategy on methods for imputing proteomics data

M Shen, YT Chang, CT Wu, SJ Parker, G Saylor… - Scientific reports, 2022 - nature.com
Missing values are a major issue in quantitative proteomics analysis. While many methods
have been developed for imputing missing values in high-throughput proteomics data, a …

Rapid multivariate analysis approach to explore differential spatial protein profiles in tissue

K Sharman, NH Patterson, A Weiss… - Journal of proteome …, 2022 - ACS Publications
Spatially targeted proteomics analyzes the proteome of specific cell types and functional
regions within tissue. While spatial context is often essential to understanding biological …

Estimation of missing values in astronomical survey data: An improved local approach using cluster directed neighbor selection

P Keerin, T Boongoen - Information Processing & Management, 2022 - Elsevier
The work presented in this paper aims to develop new imputation methods to better handle
missing values encountered in astronomical data analysis, especially the classification of …

A review of cancer data fusion methods based on deep learning

Y Zhao, X Li, C Zhou, H Pen, Z Zheng, J Chen, W Ding - Information Fusion, 2024 - Elsevier
With advancements in modern medical technology, an increasing amount of cancer-related
information can be acquired through various means, such as genomics, proteomics …