CST Guide:

Section III: Workflow Tools
chapter 17: Exploration
Protein Page
Provides information about a protein and its PTMs.
Modification Site Page
Summarizes information on single site from all records.
C. Overview:
• Brief description of protein function
• Protein type and cellular component
• Chromosomal location of human
ortholog
• Molecular function and
biological process
• Accession IDs, synonyms,
and gene symbols
• Molecular weight, isoelectric
point, and pI calculator
• Associated molecular structures
and viewer
• CST pathways and antibodies
• Structural viewer
D. Linked Resources Include:
• Pathways: STRING, Reactome,
NetworKIN
• Expression: Protein Atlas, BioGPS
• Scansite: Predictor of Kinases and
Interactors
• KinBase: Kinase Database at The
Salk Institute
• Structures: RCSB PDB, Pfam
• NextGen Protein Resource: neXtProt
E. Sites Implicated In:
• Biological and molecular regulation,
with links to associated site pages
F. Modification Sites
and Domains:
• Zoomable linear diagram
with sequence
• Domains and modification
sites mapped
• Domain names linked to Pfam
C
D
E
F
H
I
J
Curated Information Page
Experimental details on all sites in a single record.
H. Site Information:
•For most sites identified at CST, links
to MS/MS spectra are included
• Scansite predictions provide potential
kinases and binding partners
• Blast links allow site comparison
against NCBI, UniProt, or PDB
I. Experimental Summary
Sections:
May include information about how
the site was experimentally characterized;
diseases, cell lines and tissues
in which it was observed; upstream
control by treatments, receptors and
other cellular proteins, and enzymes
that may directly modify the site
(in vivo and in vitro)
J. References:
Information curated from the literature
contains links to the PubMed entry.
Information curated from MS/MS
experiments at CST or other institutions
indicates the biological sample studied
and treatments. If performed at CST
with PTMScan ® Technology, the
antibody used for peptide enrichment
prior to MS/MS is indicated.
Links to the Curated Information Page
are provided for most modification sites.
G. Table of Sites, Sequences,
and References:
• Modification sites and surrounding
sequences (+/- 7 AA) from parent
protein, orthologs, and isoforms
• Red characters indicate modified
sites with links to associated records
• First column (SS): the number
of records using site-specific,
low-throughput techniques
• Second column (MS): the number of
records using mass spectrometrybased
high-throughput techniques
G
Download PyMOL and/or Chimera script
Highlight modified residues
K
L
K. Record and Sites:
Standard bibliographic information
about the record links to its PubMed
entry. A list of modification sites
associated with this record links to
the the details curated for each site.
L. Details Curated for
each Modification Site:
• Methods used to characterize site
• Upstream Regulation
– Kinases, phosphatases, receptors
and signaling intermediates
that regulate modification
– Treatments that regulate
modification
• Downstream Regulation
– Effects on protein function and
biological processes due to
modification
– Protein-protein interactions directly
influenced by modification
• Disease Relevance of Modification
252 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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