A curated compendium of phosphorylation motifs

Amanchy, Ramars; Periaswamy, Balamurugan; Mathivanan, Suresh; Reddy, Raghunath; Tattikota, Sudhir Gopal; Pandey, Akhilesh

doi:10.1038/nbt0307-285

Cited by 349 publications

(387 citation statements)

References 11 publications

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“…This analysis led to identification of a total of 68 motifs. To determine which of these motifs have not been previously described, we took advantage of a compendium of known motifs from the literature that we have recently created (17). We observed a large number of motifs that are known to be substrate motifs for proline-directed kinases ([pS/pT]P; PxpSP) such as MAP kinases, CDK5, and GSK3 kinases (18).…”

Section: Resultsmentioning

confidence: 99%

Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

Molina

Horn

Tang

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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Electron transfer dissociation (ETD) is a recently introduced massspectrometric technique that provides a more comprehensive coverage of peptide sequences and posttranslational modifications. Here, we evaluated the use of ETD for a global phosphoproteome analysis. In all, we identified a total of 1,435 phosphorylation sites from human embryonic kidney 293T cells, of which 1,141 (Ϸ80%) were not previously described. A detailed comparison of ETD and collision-induced dissociation (CID) modes showed that ETD identified 60% more phosphopeptides than CID, with an average of 40% more fragment ions that facilitated localization of phosphorylation sites. Although our data indicate that ETD is superior to CID for phosphorylation analysis, the two methods can be effectively combined in alternating ETD and CID modes for a more comprehensive analysis. Combining ETD and CID, from this single study, we were able to identify 80% of the known phosphorylation sites in >1,000 phosphorylated peptides analyzed. A hierarchical clustering of the identified phosphorylation sites allowed us to discover 15 phosphorylation motifs that have not been reported previously. Overall, ETD is an excellent method for localization of phosphorylation sites and should be an integral component of any strategy for comprehensive phosphorylation analysis.bioinformatics ͉ motifs ͉ phosphorylation ͉ signal transduction ͉ systems biology M ost cellular processes are regulated by posttranslational modifications of proteins. For some posttranslational modifications (e.g., acetylation and tyrosine phosphorylation), identifying the modified amino acid is relatively straightforward because they are quite stable in the presence of the energy required for collisioninduced dissociation (CID) experiments. For other posttranslational modifications [e.g., O-linked N-acetylglucosamine (OGlcNAc) and phosphorylated serine and threonine residues], however, localization is substantially more difficult because the peptides either lose the modification in a charge separation process (O-GlcNAc) (1-3) or by a ␤-elimination event with a neutral loss of phosphoric acid (e.g., phosphoserine into dehydroalanine). In 1998, Zubarev et al. and Pitteri et al. (6) demonstrated that peptide cations can also be reduced and converted into radicals by reaction with radical gaseous anions, in an electron transfer process. The reduced peptides show similar fragmentation patterns as observed in ECD experiments, and the process is designated electron transfer dissociation (ETD). Although ETD has been tested in pilot experiments to localize posttranslational modifications, no large-scale analysis using ETD has yet been published.In this study, we present a global proteomic profiling of phosphopeptides subjected to fragmentation using ETD in an ion trap mass spectrometer. A total of 84,000 ETD and CID tandem MS (MS/MS) spectra from 130 liquid chromatography (LC)-MS/MS runs using three different proteolytic enzymes (Lys-C, trypsin, and Glu-C) allowed us to identify 1,435 unique phosphorylation ...

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Section: Resultsmentioning

confidence: 99%

Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

Molina

Horn

Tang

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

481

490

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“…To graphically display the identified motifs, logo-like representations were generated with Weblogo [51]. These motifs were associated with specific kinases by searching in literatures [9,21] as well as in the Arabidopsis phosphorylation site database (PhosPhAt) [15] and Human protein reference database (HPRD) [52,53].…”

Section: Phosphorylation Motif Analysismentioning

confidence: 99%

“…In total, 26 Ser motifs and 5 Thr motifs were significantly enriched (Supplemental Table 5). After associating these motifs with specific protein kinases in the literature and databases [9,15,21,52,53] The enrichment of these kinases indicates that they play crucial roles in early development and growth of Arabidopsis seedlings. 14 phosphorylation motifs (Fig.…”

Section: Discovery Of Novel Phosphorylation Motifs In Arabidopsismentioning

confidence: 99%

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A large-scale protein phosphorylation analysis reveals novel phosphorylation motifs and phosphoregulatory networks in Arabidopsis

Wang

Bian

Cheng

et al. 2013

Journal of Proteomics

100

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“…Recent advances in high-throughput methods such as tandem mass spectrometry enable rapid and direct discovery of hundreds of phosphorylation sites in a single experiment [1]. The availability of large amounts of phosphorylation sites makes it possible to perform phosphorylation motif finding using data mining techniques.…”

Section: Introductionmentioning

confidence: 99%

Motif-All: discovering all phosphorylation motifs

Yang

Guo

et al. 2011

BMC Bioinformatics

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BackgroundPhosphorylation motifs represent common patterns around the phosphorylation site. The discovery of such kinds of motifs reveals the underlying regulation mechanism and facilitates the prediction of unknown phosphorylation event. To date, people have gathered large amounts of phosphorylation data, making it possible to perform substrate-driven motif discovery using data mining techniques.ResultsWe describe an algorithm called Motif-All that is able to efficiently identify all statistically significant motifs. The proposed method explores a support constraint to reduce search space and avoid generating random artifacts. As the number of phosphorylated peptides are far less than that of unphosphorylated ones, we divide the mining process into two stages: The first step generates candidates from the set of phosphorylated sequences using only support constraint and the second step tests the statistical significance of each candidate using the odds ratio derived from the whole data set. Experimental results on real data show that Motif-All outperforms current algorithms in terms of both effectiveness and efficiency.ConclusionsMotif-All is a useful tool for discovering statistically significant phosphorylation motifs. Source codes and data sets are available at: http://bioinformatics.ust.hk/MotifAll.rar.

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A curated compendium of phosphorylation motifs

Cited by 349 publications

References 11 publications

Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

A large-scale protein phosphorylation analysis reveals novel phosphorylation motifs and phosphoregulatory networks in Arabidopsis

Motif-All: discovering all phosphorylation motifs

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