A probability-based approach for high-throughput protein phosphorylation analysis and site localization

By S. Beausoleil, J. Villén, S. Gerber, John Rush, Steven P. Gygi. Nature Biotechnology, 2006

1,587 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/f90e8e0de9083fa6e664f29cc69c3b2ded9db616

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Citations in the corpus

Systematic discovery of in vivo phosphorylation networks. (2007, background): “Identifying the position of phosphorylation sites within phosphopeptides identified with mass spectroscopy is still a difficult problem and a source of error (Beausoleil et al., 2006).”
Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization (2013, methodology): “12,30,31 Localization of diGLY sites employed a modified version of the A-score algorithm 32 as described.”
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, methodology): “While several site localization algorithms were previously described [261–263], they implement simplified approaches”
Distinct Phosphorylation Sites on the β2-Adrenergic Receptor Establish a Barcode That Encodes Differential Functions of β-Arrestin (2011, methodology): “The probability of correct phosphorylation site localization for each phosphorylation site was measured with an Ascore algorithm as described previously (43).”
Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. (2008, methodology): “After quantification as described above, we retained all phosphopeptides identified with greater than 99% certainty (Beausoleil et al., 2006).”
The UniProtKB guide to the human proteome (2016, background): “probability (PEP) of (lt)1% or a minimum PTM localization score (Ascore) of 19], only 26 497 unique peptides are validated, and 5197 phosphorylation sites are annotated in 4118 UniProtKB/Swiss-Prot entries (28, 29, 31).”
Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics (2010, background): “Alternatively, if one shifts the precursor masses of input MS/MS spectra outside of the specified mass tolerance, they cannot be correctly matched (14,20).”
Systematic and quantitative assessment of the ubiquitin modified proteome (2011, positive): “The localization of each diGly site was evaluated using a variation on the Ascore algorithm (Beausoleil et al., 2006), with minor modifications.”
Options and considerations when selecting a quantitative proteomics strategy (2010, background): “Overall, liquid chromatography tandem mass spectrometry (LC-MS/MS) with DDA is now a robust and powerful technology to detect and quantify proteins and their post-translational modifications, as exemplified by some recent large-scale studie”