Uses and misuses of the fudge factor in quantitative discovery proteomics

Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies

(2016) Cosmin Lazar et al.   JOURNAL OF PROTEOME RESEARCH

Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments

(2016) Quentin Giai Gianetto et al.   PROTEOMICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Deep Proteomic Evaluation of Primary and Cell Line Motoneuron Disease Models Delineates Major Differences in Neuronal Characteristics

(2014) Daniel Hornburg et al.   MOLECULAR & CELLULAR PROTEOMICS

In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of  -Adrenergic Receptor Signaling

(2013) A. Lundby et al.   Science Signaling

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues

(2012) Cezary Smaczniak et al.   Nature Protocols

Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics

(2012) Arne H. Smits et al.   NUCLEIC ACIDS RESEARCH

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Testing significance relative to a fold-change threshold is a TREAT

(2009) D. J. McCarthy et al.   BIOINFORMATICS

Normalization and Statistical Analysis of Quantitative Proteomics Data Generated by Metabolic Labeling

(2009) Lily Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

An Investigation on Performance of Significance Analysis of Microarray (SAM) for the Comparisons of Several Treatments with one Control in the Presence of Small-variance Genes

(2008) D. Lin et al.   BIOMETRICAL JOURNAL