CST Guide:

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Section III: Workflow Tools
Exploration
using PhosphoSitePlus® online database
How can I explore what is known about the post-translational
modifications (PTMs) occurring on my protein of interest
The PhosphoSitePlus ® (PSP) resource is a comprehensive protein modification knowledgebase,
including experimentally determined PTMs from peer-reviewed journals and analytical tools that enable
researchers to explore protein sequences, structures, mutations, pathways, and regulation. Created
with grant support from the NIH and Cell Signaling Technology (CST), and curated by CST scientists,
this database is continuously updated and features a dynamic, open, and highly interactive interface.
It is designed to facilitate the study of the roles of PTMs in normal and pathological cellular processes,
and to help accelerate the discovery of critical disease biomarkers and drug targets.
Home Page
Starting point for interacting with PhosphoSitePlus®
Users can choose from two types of Simple Searches, three Advanced Searches, and three
Browsing Interfaces.
A. Simple Searches for Protein or Kinase Substrates
In addition to the protein search, which will lead to a Protein Page, the substrate search asks the user
to enter the name of a kinase and returns a list of experimentally verified in vivo and in vitro sites
phosphorylated by the selected kinase. The preferred substrate sequences can be summarized and
viewed as a Sequence Logo.
B. Advanced Search and Browsing Options
Search interfaces give users the power to explore what is known about proteins and their PTMs.
Browse interfaces enable users to retrieve data from thousands of high-throughput (HTP) mass
spectrometry experiments.
chapter 17: Exploration
PhosphoSitePlus ® allows a researcher
to search for or download:
• Modified proteins, modification sites and sequences associated with specific protein types,
molecular weights, protein domains, treatments, tissues, diseases, cell lines, and references
• Sets of known protein kinase substrates from in vivo and in vitro experiments
• Specific sequences containing modified residues
• Scripts to generate molecular structures (PyMOL of DeLano Scientific LLC and Chimera) in which
all modified residues are labeled and color-coded
• Datasets of PTMs that overlap known mutation sites (nsSNPs), enabling the researcher to identify
those that have the potential to rewire signaling pathways
• Datasets of modification sites observed in MS-MS experiments associated with specific diseases,
cell lines, or tissues
• Complete datasets of all modification sites reported to regulate downstream processes
• Pathway datasets in Cytoscape ® of The Cytoscape Consortium and BioPAX formats
• Sequence logos and motif analyses of sets of modification sites generated within PSP or
submitted by the user
Search Proteins or Sequences by:
• Name or accession ID
• Protein type or domain
• Cellular component
• Molecular weight range
• Sequence/motif
• List of peptides
Search References by:
• Author, PubMed ID, or protein name
Search for Sites by:
• Response to treatments
• Tissues, cell line, or cell type
• Correlation with disease state
• Protein type, cellular component
• Protein function or biological process
Comparative Site Search:
• Identify sites observed in one
set of conditions but not others
• Sequence, motif, or domain
• Protein molecular weight
Downloads Datasets:
• Sites and metadata of major
modification type
• Disease mutations and genetic
variants that overlap PTMs
• Sites reported to regulate
downstream processes
• Sites regulated by specified
treatments
• Pathway information in Cytoscape ®
and BioPAX formats
Browse and Download HTP
Data Associated with:
• Specific diseases
• Cell lines
• Tissue
Sequence Analysis Tools:
• Sequence Logo Generator
• Motif Analyzer
Navigation and Content
Interactive content is delivered in four increasingly granular interfaces. Navigation between the interfaces
is seamless. Each page has links back to the Homepage.
A
Home Page; is the launch site for
searching, browsing, static downloads,
and informational pages.
Protein Page; opens when the
user selects the name of a protein
from a Search Results page
Home Page
Protein Page
Modification Site Page
B
Modification Site Page; opens
when a user clicks on a specific site
either from the Protein Page or from
a Search Results page.
Curated Information Page
Curated Information Page;
opens when a user clicks on a
specific reference on a Modification
Site Page, and presents the most
granular information in PSP.
250 For Research Use Only. Not For Use in Diagnostic Procedures. See pages 302 & 303 for Pathway Diagrams, Application, and Reactivity keys.
www.cellsignal.com/exploration
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