In this section
@article{Pruktanakul:2026:10.1021/acs.jproteome.6c00019,
author = {Pruktanakul, T and Lynham, S and Chen, H and Yin, X and Mayr, M and Theofilatos, K},
doi = {10.1021/acs.jproteome.6c00019},
journal = {Journal of Proteome Research},
title = {ComparativeAnalysis of Data Processing Tools forMass Spectrometry Proteomics in Cardiovascular Research},
url = {http://dx.doi.org/10.1021/acs.jproteome.6c00019},
year = {2026}
}
TY - JOUR
AB - <jats:title>Abstract</jats:title> <jats:p>Mass spectrometry-based proteomics requires advanced data processing tools, yet most comparative studies have relied on noncardiovascular data sets or standard protein mixtures, limiting their relevance to cardiovascular research. We systematically compared three label-free data-dependent acquisition (DDA) tools (FragPipe, MaxQuant, and Proteome Discoverer) and five data-independent acquisition (DIA) tools (DIA-NN, DIA-Umpire, MSFragger-DIA, MaxDIA, and Spectronaut) using real-world cardiovascular tissue and blood-derived proteomics data sets. FragPipe and Spectronaut generally achieved the greatest quantitative proteome coverage among the evaluated DDA and DIA tools, respectively, particularly in cardiovascular tissue data sets, although tool rankings varied across sample types and proteome subsets. Despite differences in identification and quantification performance, peptide physicochemical characteristics were broadly similar across tools. Integration of complementary differential expression outputs increased differentially expressed protein detection in several data sets while maintaining agreement with the main results. These findings provide practical guidance for selecting data processing tools in cardiovascular proteomics and support the use of integrative approaches to maximize biological information from proteomics data sets.</jats:p>
AU - Pruktanakul,T
AU - Lynham,S
AU - Chen,H
AU - Yin,X
AU - Mayr,M
AU - Theofilatos,K
DO - 10.1021/acs.jproteome.6c00019
PY - 2026///
SN - 1535-3893
TI - ComparativeAnalysis of Data Processing Tools forMass Spectrometry Proteomics in Cardiovascular Research
T2 - Journal of Proteome Research
UR - http://dx.doi.org/10.1021/acs.jproteome.6c00019
UR - https://doi.org/10.1021/acs.jproteome.6c00019
ER -