LFQ-Based Peptide and Protein Intensity Differential Expression Analysis

Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform t...

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Bibliographic Details
Published in:Journal of proteome research Vol. 22; no. 6; p. 2114
Main Authors: Bai, Mingze, Deng, Jingwen, Dai, Chengxin, Pfeuffer, Julianus, Sachsenberg, Timo, Perez-Riverol, Yasset
Format: Journal Article
Language:English
Published: United States 02.06.2023
Subjects:
Mass Spectrometry - methods
Peptides - analysis
Proteins - analysis
Proteomics - methods
Software
protein fold changes
imputation and normalization algorithms
data analysis
mass spectrometry proteomics
protein expression
ISSN:1535-3907, 1535-3907
Online Access:Get more information
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Summary:Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings.
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ISSN:1535-3907
1535-3907
DOI:10.1021/acs.jproteome.2c00812