蛋白质磷酸化修饰相关计算资源汇总

深藏阁楼爱情的钟 2022-05-14 23:04 317阅读 0赞

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       <td> <p>For publication of results, please cite the following article:</p> 
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           <td> <a href="http://www.benthamdirect.org/pages/b_viewarticle.php?3161111" rel="nofollow"><img style="border:0pt none;" src="http://www.benthamdirect.org/adminPages/uploads/CPPS.gif" alt="CPPS" width="94" height="121"></a> </td> 
           <td> <p><strong>A summary of computational resources for protein phosphorylation</strong> .<a href="mailto:xueyu@ustc.edu.cn" rel="nofollow">Yu Xue</a> , Xinjiao Gao, Cao Jun, Liu Zexian, Changjiang Jin, Longping Wen, Xuebiao Yao, and <a href="mailto:renjian@ustc.edu.cn" rel="nofollow">Jian Ren</a> . <strong>Current Protein &amp; Peptide Science. 2010</strong> ; 11(6):485-496</p> <p><a href="http://mcponline.highwire.org/cgi/content/full/M700574-MCP200/DC1" rel="nofollow"></a> </p> </td> 
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**Introduction** :

Protein **phosphorylation** is the most ubiquitous post-translational modification (PTM), and plays important roles in most of biological processes. Identification of site-specific phosphorylated substrates is fundamental for understanding the molecular mechanisms of phosphorylation. Besides experimental approaches, prediction of potential candidates with computational methods has also attracted great attention for its convenience and fast-speed. In this review, we present a comprehensive but brief summarization of computational resources of protein phosphorylation, including phosphorylation databases, prediction of non-specific or organism-specific phosphorylation sites, prediction of kinase-specific phosphorylation sites or phospho-binding motifs, and other tools. A testing data set prepared from [Phospho.ELM][] 6.0 is available at: **[Comparison\_data][Comparison_data]** .

We apologized that the computational studies without any web links of databases or tools will not be included in this compendium, since it's not easy for experimentalists to use studies directly. We are grateful for users feedback. Please inform **[Prof. Yu Xue ][Prof. Yu Xue]** or **[Prof. Jian Ren ][Prof. Jian Ren]** to add, remove or update one or multiple web links below.

**Index** :

[**<1> Phosphorylation Databases** ][1_ Phosphorylation Databases_]

[ ][Link 1]

[**<2> Prediction of non-specific or organism-specific phosphorylation sites** ][Link 1]

[ ][Link 1] [ ][Link 2]

[**<3> Prediction of kinase-specific phosphorylation sites or phospho-binding motifs** ][Link 2]

[ ][Link 2] [ ][Link 3]

[**<4> Miscellaneous tools** ][Link 3]

[ ][Link 3] [ ][Link 4]

[**<5> Detection of potential phosphorylation sites from mass spectrometry data** ][Link 4]

[ ][Link 4]

==================================================================================

**<1> Phosphorylation Databases** :

1. [**Phospho.ELM 8.3 (PhosphoBase)** ][Phospho.ELM] : contains 5,115 experimentally verified phosphorylated proteins from different species with 2,746 tyrosine, 15,972 serine and 3,283 threonine sites. All instances were manually collected from scientific literature ([Diella, *et al.* , 2004][Diella_ _et al._ _ 2004] ; [Diella, *et al.* , 2008][Diella_ _et al._ _ 2008] ).

2. [**PhosphoSitePlus** ][PhosphoSitePlus_] : a new version of PhosphoSite, is a web-based database to collect protein modification sites, including protein phosphorylation sites from scientific literature as well as high-throughput discovery programs. Currently, PhosphoSitePlus contains 78,022 phosphorylation sites ([Hornbeck, *et al.* , 2004][Hornbeck_ _et al._ _ 2004] ).

3. [**PhosphoNET** ][PhosphoNET_] : PhosphoNET presently holds data on more than 74,000 phosphorylation sites in over 12,400 human proteins that have been collected from the scientific literature and other reputable websites. It features direct links to several other useful websites, and will continue to expand as a useful portal for phosphoproteomics information.

4. [**HPRD release 9**  ][HPRD release 9_] : HPRD currently contains information for 16,972 PTMs which belong to various categories with phosphorylation (10,858), dephosphorylation (3,118) and glycosylation (1,860) forming the majority of the annotated PTMs. At least one enzyme responsible for PTMs has been annotated for 8,960 PTMs, which resulted in the documentation of 7,253 enzyme - substrate relationships ([Keshava Prasad, *et al* ., 2009][Keshava Prasad_ _et al_ ._ 2009] ).

5. [**PHOSIDA** ][PHOSIDA_] ([**Mirror website** ][PHOSIDA_] ): a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts non-specific phosphosites ([Gnad, *et al.* , 2007][Gnad_ _et al._ _ 2007] ; [Gnad, *et al.* , 2009][Gnad_ _et al._ _ 2009] ).

6. [**PhosphoPep v2.0** ][PhosphoPep v2.0_] : contains MS-derived phosphorylation data from 4 different organisms, including fly (*Drosophila melanogaster* ), human (*Homo sapiens* ), worm (*Caenorhabditis elegans* ), and yeast (*Saccharomyces cerevisiae* ) ([Bodenmiller, *et al.* , 2008][Bodenmiller_ _et al._ _ 2008] ).

7. [**PhosPhAt 3.0** ][PhosPhAt 3.0_] : contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups with 6,282 phosphopeptides ([Heazlewood, *et al.* , 2008][Heazlewood_ _et al._ _ 2008] ; [ Durek, *et al.* , 2010][Durek_ _et al._ _ 2010] ).

8. [**P(3)DB 1.1** ][P_3_DB 1.1_] : provides a database of protein phosphorylation data from multiple plants. The database was initially constructed with a dataset from oilseed rape, including 14,670 nonredundant phosphorylation sites from 6382 substrate proteins ([Gao, *et al.* , 2009][Gao_ _et al._ _ 2009] ).

9. [**Swiss-Prot knowledge base** ][Swiss-Prot knowledge base_] ([**Mirror website** ][Mirror website_] ): for each protein annotation, the "Amino acid modifications" in the "Sequence annotation (Features)" section collected the post-translational modification information of proteins ([Farriol-Mathis, *et al.* , 2004][Farriol-Mathis_ _et al._ _ 2004] ).

10. [**dbPTM 2.0** ][dbPTM 2.0_] : integrates experimentally verified PTMs from several databases, and to annotate the predicted PTMs on Swiss-Prot proteins ([Lee, *et al.* , 2006][Lee_ _et al._ _ 2006] ).

11. [**SysPTM 1.1** ][SysPTM 1.1_] ([**Mirror website** ][Mirror website_ 1] ): provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools. ([Li, *et al.* , 2009][Li_ _et al._ _ 2009] ).

12. [**PhosphoPOINT** ][PhosphoPOINT_] : is a comprehensive human kinase interactome and phospho-protein database, containing 4195 phospho-proteins with a total of 15,738 phosphorylation sites ([Yang, *et al.* , 2008][Yang_ _et al._ _ 2008] ).

13. **[NetworKIN 1.0][]** (**[NetworKIN-2.0 beta version][]** ): is a method for predicting *in vivo* kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins. It's a great resource and open a door for computational discovering of phospho-regulatory network ([Linding, *et al.* , 2007][Linding_ _et al._ _ 2007] ; [Linding, *et al.* , 2008][Linding_ _et al._ _ 2008] ).

14. [**Phospho3D** ][Phospho3D_] : is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level ([Zanzoni, *et al.* , 2007][Zanzoni_ _et al._ _ 2007] ).

15. [**PepCyber :P~Pep 1.2** ][PepCyber _P_Pep 1.2_] : is a database of human protein-protein interactions mediated by 10 classes of phosphoprotein binding domains (PPBDs) ([Gong, *et al.* , 2008][Gong_ _et al._ _ 2008] ).

16. [**PhosphoVariant** ][PhosphoVariant_] : a database for human phosphovariants, which were defined as genetic variations that change phosphorylation sites or their interacting kinases ([Ryu, *et al* ., 2009][Ryu_ _et al_ ._ 2009] ).

17. **[ProMEX][]** : a mass spectral reference database for proteins and protein phosphorylation sites, containing 4,557 manually validated spectra associated with 4,226 unique peptides from 1,367 proteins ([Hummel, *et al* ., 2009][Hummel_ _et al_ ._ 2009] ).

18. **[PlantsP][]** : contains more than 300 phosphorylation sites from Arabidopsis thaliana plasma membrane proteins ([Nühse, *et al* ., 2009][N_hse_ _et al_ ._ 2009] ).

19. **[LymPHOS][]** : a phosphosite database of primary human T cells, with 342 phosphorylation sites mapping to more than 200 gene sequences ([Ovelleiro, *et al* ., 2009][Ovelleiro_ _et al_ ._ 2009] ).

20. **[PhosSNP 1.0][]** : a genome-wide analysis of genetic polymorphisms that influence protein phosphorylation in *H. Sapiens* . It was estimated that ~69.76% of nsSNPs (non-synonymous SNPs) are potential phosSNPs (Phosphorylation-related SNPs) (64, 035) in 17, 614 proteins ([Ren, *et al* ., 2010][Ren_ _et al_ ._ 2010] ).

21. **[The Phosphorylation Site Database][]** : provides ready access to information from the primary scientific literature concerning those proteins from prokaryotic organisms, i.e., the members of the domains Archaea and Bacteria, that have been reported to undergo covalent phosphorylation on the hydroxyl side chains of serine, threonine, and/or tyrosine residues ([Wurgler-Murphy, *et al* ., 2004][Wurgler-Murphy_ _et al_ ._ 2004] ).

22. **[PhosphoGRID][]** : a database of experimentally verified in vivo phosphorylation sites curated from the *S. cerevisiae* primary literature. PhosphoGRID records the positions of over 5000 specific phosphorylated residues on 1495 gene products. ([Stark, *et al* ., 2004][Stark_ _et al_ ._ 2004] ).

**<2> Prediction of non-specific or organism-specific phosphorylation sites** :

1. [**NetPhos 2.0** ][NetPhos 2.0_] : produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins ([Blom, *et al.* , 1999][Blom_ _et al._ _ 1999] ).

2. [**CRP** ][CRP_] : **C** leaved **R** adioactivity of **P** hosphopeptides. CRP performs an *in silico* proteolytic cleavage of the sequence and reports the predicted Edman cycles in which radioactivity would be observed if a given serine, threonine or tyrosine will be phosphorylated ([Mackey, *et al.* , 2003][Mackey_ _et al._ _ 2003] ).

3. [**DISPHOS 1.3** ][DISPHOS 1.3_] : uses disorder information to improve the discrimination between phosphorylation and non-phosphorylation sites, and predicts serine, threonine and tyrosine phosphorylation sites in proteins ([Iakoucheva, *et al.* , 2004][Iakoucheva_ _et al._ _ 2004] ).

4. [**NetPhosYeast 1.0** ][NetPhosYeast 1.0_] : predicts serine and threonine phosphorylation sites in yeast proteins ([Ingrell, *et al.* , 2007)][Ingrell_ _et al._ _ 2007] .

5. **[NetPhosBac 1.0][]** : NetPhosBac 1.0 server predicts serine and threonine phosphorylation sites in bacterial proteins ([Miller *et al* . 2009][Miller _et al_ . 2009] ).

6. [**PhosPhAt 3.0** ][PhosPhAt 3.0_] : They utilized a set of 802 experimentally validated serine phosphorylation sites as the training data set in their 2.2 version, while with additional 1,818 threonine phosphorylation sites and 676 tyrosine sites in *Arabidopsis*  to develop their 3.0 predictor for phosphorylation sites in *Arabidopsis* ([Heazlewood, *et al.* , 2008][Heazlewood_ _et al._ _ 2008] ; [ Durek, *et al.* , 2010][Durek_ _et al._ _ 2010] ).

7. [**PHOSIDA** ][PHOSIDA_ 1] ([**Mirror website** ][PHOSIDA_] ): a predictor based on more than 5,000 high confidence phosphosites, with the Support vector machines (SVMs) algorithm ([Gnad, *et al.* , 2007][Gnad_ _et al._ _ 2007] ).

8. **GANNPhos** : uses a genetic algorithm integrated neural network (GANN) algorithm ([Tang, *et al.* , 2007][Tang_ _et al._ _ 2007] ). **The tool is not available.**

9. **PHOSITE** : is based on the case-based sequence analysis ([Koenig and Grabe, 2004][Koenig and Grabe_ 2004] ). **The tool is not available.**

**<3> Prediction of kinase-specific phosphorylation sites or phospho-binding motifs** :

1. [**GPS 2.1**  ][GPS 2.1_] **![GPS][]** :The current version of GPS system. We renamed the tool as the **G** roup-based **P** rediction **S** ystem. GPS 2.1 software was implemented in JAVA and could predict kinase-specific phosphorylation sites for 408 human Protein Kinases in hierarchy ([Xue, *et al.* , 2008][Xue_ _et al._ _ 2008] ).

2. **[GPS 1.10][] ![GPS][]** : The old version of GPS. We designed a novel algorithm GPS (Group-based Phosphorylation sites Prediction) and construct an easy-to-use web server for the experimentalists ([Xue, *et al.* , 2005][Xue_ _et al._ _ 2005] ; [Zhou, *et al.* , 2004][Zhou_ _et al._ _ 2004] ).

3. [**PPSP 1.0**  ][PPSP 1.0_] **![GPS][]** :We also developed another online program for prediction of kinase-specific phosphorylation sites, implemented in Baysian Decision Theory (BDT) ([Xue, *et al* ., 2006][Xue_ _et al_ ._ 2006] ).

4. **[ScanProsite][]** : consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them ([de Castro, *et al.* , 2006][de Castro_ _et al._ _ 2006] ; [Hulo, *et al.* , 2008][Hulo_ _et al._ _ 2008] ).

5. **[ELM][]** : is a resource for predicting functional sites in eukaryotic proteins ([Puntervoll, *et al.* , 2003][Puntervoll_ _et al._ _ 2003] ).

6. **[Minimotif Miner][]** : analyzes protein queries for the presence of short functional motifs that, in at least one protein, has been demonstrated to be involved in posttranslational modifications (PTM), binding to other proteins, nucleic acids, or small molecules, or proteins trafficking ([Balla, *et al.* , 2006][Balla_ _et al._ _ 2006] ; [Rajasekaran, *et al.* , 2009][Rajasekaran_ _et al._ _ 2009] ).

7. [**PhosphoMotif Finder** ][PhosphoMotif Finder_] : contains known kinase/phosphatase substrate as well as binding motifs that are curated from the published literature. It reports the PRESENCE of any literature-derived motif in the query sequence ([Amanchy, *et al.* , 2007][Amanchy_ _et al._ _ 2007] ).

8. [**PREDIKIN 1.0** ][PREDIKIN 1.0_] : produces a prediction of substrates for serine/threonine protein kinases based on the primary sequence of a protein kinase catalytic domain ([Brinkworth, *et al.* , 2003][Brinkworth_ _et al._ _ 2003] ).

9. [**Predikin & PredikinDB 2.0** ][Predikin _ PredikinDB 2.0_] : consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences ([Saunders, *et al.* , 2008][Saunders_ _et al._ _ 2008] ; [Saunders and Kobe, 2008][Saunders and Kobe_ 2008] ).

10. [**ScanSite 2.0** ][ScanSite 2.0_] : searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains ([Obenauer, *et al.* , 2003][Obenauer_ _et al._ _ 2003] ).

11. [**NetPhosK 1.0** ][NetPhosK 1.0_] : produces neural network predictions of kinase specific eukaryotic protein phosphoylation sites. Currently NetPhosK covers the following kinases: PKA, PKC, PKG, CKII, Cdc2, CaM-II, ATM, DNA PK, Cdk5, p38 MAPK, GSK3, CKI, PKB, RSK, INSR, EGFR and Src ([Blom, *et al.* , 2004][Blom_ _et al._ _ 2004] ).

12. [**PredPhospho 1.0** ][PredPhospho 1.0_] : implemented in SVM algorithm, could predict kinase-specific phosphorylation sites for 4 kinase groups and 4 kinase families, respectively ([Kim, *et al.* , 2004][Kim_ _et al._ _ 2004] ).

13. [**PredPhospho 2.0** ][PredPhospho 2.0_] : enhance version of PredPhospho predictor, which was still implemented in SVM algorithm, for 7 kinase groups and 18 kinase families, respectively ([Ryu, *et al* ., 2009][Ryu_ _et al_ ._ 2009] ).

14. [**KinasePhos 1.0** ][KinasePhos 1.0_] : predicts kinase-specific phosphorylation sites within given protein sequences. Profile Hidden Markov Model (HMM) is applied for learning to each group of sequences surrounding to the phosphorylation residues ([Huang, *et al.* , 2005][Huang_ _et al._ _ 2005] ).

15. [**KinasePhos 2.0** ][KinasePhos 2.0_] : New version of kinase-specific phosphorylation site prediction tool that is based the sequenece-based amino acid coupling-pattern analysis and solvent accessibility as new features of SVM (support vector machine) ([Wong, *et al.* , 2007][Wong_ _et al._ _ 2007] ).

16. [**PhoScan** ][PhoScan_] : predicts of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach ([Li, *et al.* , 2007][Li_ _et al._ _ 2007] ).

17. [**pkaPS** ][pkaPS_] : Prediction of protein kinase A phosphorylation sites using the simplified kinase binding model ([Neuberger, *et al.* , 2007][Neuberger_ _et al._ _ 2007] ).

18. [**CRPhos 0.8** ][CRPhos 0.8_] : Prediction of kinase-specific phosphorylation sites using conditional random fields. Its source code is free for academic research and could be compiled in Linux/Unix OS ([Dang, *et al.* , 2008][Dang_ _et al._ _ 2008] ).

19. [**AutoMotif 2.0** ][AutoMotif 2.0_] : allows for identification of PTM (post-translational modification) sites, including phosphorylation sites in proteins. The AutoMotif Server 2.0 was trained support vector machine (SVM) for each type of PTM separately on proteins of the Swiss-Prot database (version 42.0) ([Plewczynski, *et al.* , 2005][Plewczynski_ _et al._ _ 2005] ; [Plewczynski, *et al.* , 2008][Plewczynski_ _et al._ _ 2008] ).

20. [**MetaPredPS** ][MetaPredPS_] : Meta-predictors make predictions by organizing and processing the predictions produced by several other predictors in a defined problem domain ([Wan, *et al.* , 2008][Wan_ _et al._ _ 2008] ).

21. **[SMALI][]** : searches for peptide ligands in human proteins that are likely to bind to SH2 domains ([Huang, *et al.* , 2008][Huang_ _et al._ _ 2008] ; [Li, *et al.* , 2008][Li_ _et al._ _ 2008] ).

22. [**NetPhorest** ][NetPhorest_] : is a non-redundant collection of 125 sequence-based classifiers for linear motifs in phosphorylation-dependent signaling. The collection contains both family-based and gene-specific classifiers ([Miller, *et al.* , 2008][Miller_ _et al._ _ 2008] ).

23. **SiteSeek** : is trained using a novel compact evolutionary and hydrophobicity profile to detect possible protein phosphorylation sites for a target sequence ([Yoo, *et al.* , 2008][Yoo_ _et al._ _ 2008] ). **The tool is not available.**

24. [**PostMod** ][PostMod_] : is a predict sever for phosphorylation sites. The authors combined physicochemical information, motif information, and evolutionary information by simply comaparing sequence similarities, and could predict phosphorylation sites for 48 different kinases ([Jung, *et al.* , 2010][Jung_ _et al._ _ 2010] ).

**<4> Miscellaneous tools** :

1. **[DOG 1.0 ][DOG 1.0]** **![GPS][]** :prepares publication-quality figures of protein domain structures. The scale of a protein domain and the position of a functional motif/site will be precisely calculated ([Ren, *et al.* , 2009][Ren_ _et al._ _ 2009] ).

2. [**Motif-X** ][Motif-X_] : is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background ([Schwartz and Gygi, 2005][Schwartz and Gygi_ 2005] ).

3. [**Scan-X** ][Scan-X_] : is a software tool designed to find motifs (identified using motif-x) within any sequence data set. The first large scale scan was performed using all available human, mouse, fly and yeast phosphorylation and acetylation data to perform a scan for undiscovered sites ([Schwartz, *et al.* , 2008][Schwartz_ _et al._ _ 2008] ).

4. [**MoDL** ][MoDL_] : finds mutliple motifs in a set of phosphorylated peptides ([Ritz, *et al.* , 2009][Ritz_ _et al._ _ 2009] ).

5. **[PhosphoBlast][]** : allows the user to submit a protein query to search against the curated dataset of phosphorylated peptides ([Wang and Klemke, 2008][Wang and Klemke_ 2008] ).

6. **[RLIMS-P][]** : is a rule-based text-mining program specifically designed to extract protein phosphorylation information on protein kinase, substrate and phosphorylation sites from the abstracts ([Hu, *et al.* , 2005][Hu_ _et al._ _ 2005] ; [Yuan, *et al.* , 2006][Yuan_ _et al._ _ 2006] ).

7. **[KEA][]** : Kinase enrichment analysis (KEA) is a web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them ([Lachmann and Ma'ayan, 2009][Lachmann and Ma_ayan_ 2009] ).

**<5> Detection of potential phosphorylation sites from mass spectrometry data**  :

1. **[PhosphoScore][]** : is a phosphorylation assignment program that is compatible with all levels of tandem mass spectrometry spectra (MSn) generated through the Bioworks/Sequest platform. The program utilizes a “cost function” which takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore was written in Java ([Ruttenberg, *et al.* , 2008][Ruttenberg_ _et al._ _ 2008] ).

2. **[Ascore][]** : measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra ([Beausoleil, *et al.* , 2006][Beausoleil_ _et al._ _ 2006] ).

3. [**Colander** ][Colander_] : a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search ([Lu, *et al.* , 2008][Lu_ _et al._ _ 2008] ).

4. [**DeBunker** ][Colander_] : a SVM-based software, which could automatically validate phosphopeptide identifications from tandem mass spectra ([Lu, *et al.* , 2007][Lu_ _et al._ _ 2007] ).

5. **[APIVASE 2.2][]** : was developed for phosphopeptide validation by combining the information obtained from MS2 spectra and its corresponding neutral loss MS3 spectra ([Jiang, *et al.* , 2008][Jiang_ _et al._ _ 2008] ).

6. **[InsPecT][]** : a new scoring function was developed for phosphorylated peptide tandem mass spectra for ion-trap instruments, without the need for manual validation ([Payne, *et al.* , 2008][Payne_ _et al._ _ 2008] ).

7. **[Phosphopeptide FDR Estimator ][Phosphopeptide FDR Estimator]** : is designed for analysis of phosphopeptide LC-MS/MS data ([Du, *et al.* , 2008][Du_ _et al._ _ 2008] ). **The tool is not available.**

8. **PhosTShunter** : a fast and reliable tool to detect phosphorylated peptides in liquid chromatography Fourier transform tandem mass spectrometry data sets ([Kocher, *et al.* , 2006][Kocher_ _et al._ _ 2006] ). **The tool is not available.**

9. **PhosphoScan** : a probability-based method for phosphorylation site prediction using MS2/MS3 pair information ([Wan, *et al.* , 2008][Wan_ _et al._ _ 2008 1] ). **The tool is not available.**

10. **[ArMone][]** : a new scoring function was developed for phosphorylated peptide tandem mass spectra for ion-trap instruments, without the need for manual validation ([Jiang, *et al.* , 2010][Jiang_ _et al._ _ 2010] ).

[Phospho.ELM]: http://phospho.elm.eu.org/
[Comparison_data]: http://gps.biocuckoo.org/Comparison_data.tgz
[Prof. Yu Xue]: mailto:xueyu@mail.hust.edu.cn
[Prof. Jian Ren]: mailto:renjian.sysu@gmail.com
[1_ Phosphorylation Databases_]: http://gps.biocuckoo.org/links.php#l1
[Link 1]: http://gps.biocuckoo.org/links.php#l2
[Link 2]: http://gps.biocuckoo.org/links.php#l3
[Link 3]: http://gps.biocuckoo.org/links.php#l4
[Link 4]: http://gps.biocuckoo.org/links.php#l5
[Diella_ _et al._ _ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15212693
[Diella_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17962309
[PhosphoSitePlus_]: http://www.phosphosite.org/
[Hornbeck_ _et al._ _ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15174125
[PhosphoNET_]: http://www.phosphonet.ca/
[HPRD release 9_]: http://www.hprd.org/
[Keshava Prasad_ _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18988627
[PHOSIDA_]: http://www.phosida.com/
[Gnad_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18039369
[Gnad_ _et al._ _ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19795423
[PhosphoPep v2.0_]: http://www.phosphopep.org/
[Bodenmiller_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19060867
[PhosPhAt 3.0_]: http://phosphat.mpimp-golm.mpg.de/
[Heazlewood_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17984086
[Durek_ _et al._ _ 2010]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19880383
[P_3_DB 1.1_]: http://digbio.missouri.edu/p3db/
[Gao_ _et al._ _ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18931372
[Swiss-Prot knowledge base_]: http://www.expasy.org/
[Mirror website_]: http://www.uniprot.org/
[Farriol-Mathis_ _et al._ _ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15174124
[dbPTM 2.0_]: http://dbptm.mbc.nctu.edu.tw/
[Lee_ _et al._ _ 2006]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16381945
[SysPTM 1.1_]: http://www.biosino.org.cn/SysPTM/
[Mirror website_ 1]: http://lifecenter.sgst.cn/SysPTM/
[Li_ _et al._ _ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19366988
[PhosphoPOINT_]: http://kinase.bioinformatics.tw/
[Yang_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18689816
[NetworKIN 1.0]: http://networkin.info/search.php
[NetworKIN-2.0 beta version]: http://networkin.info/version_2_0/search.php
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[Zanzoni_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17142231
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[Gong_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18160410
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[Ryu_ _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/pubmed/19139070
[ProMEX]: http://promex.pph.univie.ac.at/promex/
[Hummel_ _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/pubmed/17587460
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[LymPHOS]: http://www.lymphos.org/
[Ovelleiro_ _et al_ ._ 2009]: http://www.ncbi.nlm.nih.gov/pubmed/19639593
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[Ren_ _et al_ ._ 2010]: http://www.ncbi.nlm.nih.gov/pubmed/19995808
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[Wurgler-Murphy_ _et al_ ._ 2004]: http://www.ncbi.nlm.nih.gov/pubmed/15174126
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[Stark_ _et al_ ._ 2004]: http://www.ncbi.nlm.nih.gov/pubmed/20428315
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[Blom_ _et al._ _ 1999]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10600390
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[Mackey_ _et al._ _ 2003]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824437
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[Iakoucheva_ _et al._ _ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14960716
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[Ingrell_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17282998
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[Miller _et al_ . 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19053140
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[Tang_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17652129
[Koenig and Grabe_ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15297298
[GPS 2.1_]: http://gps.biocuckoo.org/
[GPS]: /images/20220515/5967a53992e0402281ef3894d1cab6a1.png
[Xue_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18463090
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[Xue_ _et al._ _ 2005]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980451
[Zhou_ _et al._ _ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15555589
[PPSP 1.0_]: http://ppsp.biocuckoo.org/
[Xue_ _et al_ ._ 2006]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16549034
[ScanProsite]: http://www.expasy.org/prosite/
[de Castro_ _et al._ _ 2006]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16845026
[Hulo_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18003654
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[Puntervoll_ _et al._ _ 2003]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824381
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[Balla_ _et al._ _ 2006]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16489333
[Rajasekaran_ _et al._ _ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18978024
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[Amanchy_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17344875
[PREDIKIN 1.0_]: http://florey.biosci.uq.edu.au/kinsub/predikin.htm
[Brinkworth_ _et al._ _ 2003]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12502784
[Predikin _ PredikinDB 2.0_]: http://predikin.biosci.uq.edu.au/pkr/
[Saunders_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18501020
[Saunders and Kobe_ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18477637
[ScanSite 2.0_]: http://scansite.mit.edu/
[Obenauer_ _et al._ _ 2003]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824383
[NetPhosK 1.0_]: http://www.cbs.dtu.dk/services/NetPhosK/
[Blom_ _et al._ _ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15174133
[PredPhospho 1.0_]: http://www.nih.go.kr/predphospho/proteo/html/inc_PredPhospho.htm
[Kim_ _et al._ _ 2004]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15231530
[PredPhospho 2.0_]: http://www.nih.go.kr/phosphovariant/html/seq_input_predphospho2.htm
[KinasePhos 1.0_]: http://kinasephos.mbc.nctu.edu.tw/
[Huang_ _et al._ _ 2005]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980458
[KinasePhos 2.0_]: http://kinasephos2.mbc.nctu.edu.tw/
[Wong_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17517770
[PhoScan_]: http://bioinfo.au.tsinghua.edu.cn/phoscan/
[Li_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17680694
[pkaPS_]: http://mendel.imp.ac.at/sat/pkaPS/
[Neuberger_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17222345
[CRPhos 0.8_]: http://www.ptools.ua.ac.be/CRPhos/
[Dang_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18940828
[AutoMotif 2.0_]: http://ams2.bioinfo.pl/
[Plewczynski_ _et al._ _ 2005]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15728119
[Plewczynski_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17994256
[MetaPredPS_]: http://metapred.umn.edu/MetaPredPS/index.php
[Wan_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18234718
[SMALI]: http://lilab.uwo.ca/SMALI.htm
[Huang_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17956856
[Li_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18424801
[NetPhorest_]: http://netphorest.info/
[Miller_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18765831
[Yoo_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18541042
[PostMod_]: http://biodb.kaist.ac.kr/PTM/
[Jung_ _et al._ _ 2010]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20122181
[DOG 1.0]: http://dog.biocuckoo.org/
[Ren_ _et al._ _ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19153597
[Motif-X_]: http://motif-x.med.harvard.edu/motif-x.html
[Schwartz and Gygi_ 2005]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16273072
[Scan-X_]: http://motif-x.med.harvard.edu/scan-x.html
[Schwartz_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18974045
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[Ritz_ _et al._ _ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18996944
[PhosphoBlast]: http://phospho.elm.eu.org/pELMBlastSearch.html
[Wang and Klemke_ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17934212
[RLIMS-P]: http://pir.georgetown.edu/pirwww/iprolink/rlimsp.shtml
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[KEA]: http://amp.pharm.mssm.edu/lib/kea.jsp
[Lachmann and Ma_ayan_ 2009]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19176546
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[Ruttenberg_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18543960
[Ascore]: http://ascore.med.harvard.edu/
[Beausoleil_ _et al._ _ 2006]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16964243%20
[Colander_]: http://fields.scripps.edu/download.php
[Lu_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18563924
[Lu_ _et al._ _ 2007]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17297928
[APIVASE 2.2]: http://bioanalysis.dicp.ac.cn/proteomics/software/APIVASE.html
[Jiang_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18314942
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[Payne_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18563926
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[Du_ _et al._ _ 2008]: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18422353
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