Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.

ABSTRACT: Recent advances in mass spectrometry-based proteomics enable the acquisition of increasingly large datasets within relatively short times, which exposes bottlenecks in the bioinformatics pipeline. Although peptide identification is already scalable, most label-free quantification (LFQ) algorithms scale quadratic or cubic with the sample numbers, which may even preclude the analysis of large-scale data. Here we introduce directLFQ, a ratio-based approach for sample normalization and the calculation of protein intensities. It estimates quantities via aligning samples and ion traces by shifting them on top of each other in logarithmic space. Importantly, directLFQ scales linearly with the number of samples, allowing analyses of large studies to finish in minutes instead of days or months. We

SUBMITTER: Ammar C 

PROVIDER: S-EPMC10315922 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature