Using random peptides to identify and isolate specific antibodies Paper

2015-03-01

azim58 - Using random peptides to identify and isolate specific
antibodies Paper


Title of Paper (oldest to newest): Using random peptides to identify and isolate specific
antibodies
Mining random space for real antibody epitopes
Using random sequence space to define cognate antibody ligands
Random sequence mimotopes capture immune-specific antibodies and predict
epitope motifs
Random sequence mimotopes capture immune-specific antibodies
Mimotope Screen with Non-natural Sequence Peptide-Arrays


aka
smc paper with kathy and shen

Location of files:
C:\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1

!Make sure to find most recent version of paper!!


most recent version of paper
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\03-10-2014d1137 Shen's revisions\SMC1Afs_Mimotopes 03082014.docx"

Most recent version of collection of files to send out to people




Version of document in which I had some notes for the sources of the figures



some records of revisions 


-"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\1-16-14 revisions from Shen\SMC1Afs_Mimotopes 0106-by Shen revised-by Kurt-by shen accepted .docx"


--Shen revised the paper and then sent it to Kathy.  For some reason in this document there are a lot of words that are accidentally combined without a space between them. 01-16-2014


most recent version of figures
C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 01-05-2014d1213

Table
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Table 1.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Table 2.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Supplementary Table 1.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Supplementary Table 2.docx"

Equation
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 01-05-2014d1213\Equation 1.docx"

Highlights
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\Highlights\Highlights 1-5-14.docx"

Keywords
Mimotope, random peptide, epitope, antibody, microarray

Abbreviations
ELISA, DNA, SPOT, SMC1A, SMC1Afs, KLH, PBST, BSA, HRP, TMB, SMCfs, TBST, PBS, TRIS
Abbreviations that are not standard in this field
Abbreviations listed in paper


Files to send to others
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\01-02-2014d1019 revision\SMC1Afs_Mimotopes 01-02-2014d1020.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 01-05-2014d1213\All Figures 1-5-13.pdf"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Table 1.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Table 2.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 01-05-2014d1213\Equation 1.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\Highlights\Highlights 1-5-14.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Supplementary Table 1.docx"
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\Supplementary Table 2.docx"


Paper of mine that I can refer to when preparing this document
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\3p_library\paper\A microarray method for identifying tumor antigens by screening a tumor cDNA expression library against cancer sera.docx"




Desired Journal for Paper: see Journal of Immunological Methods article
structure
Mini Checklist for Paper
prepare 6 keywords
prepare Highlights
define abbreviations
acknowledgements
Make sure tables and figures have the accepted font (accepted fonts are
Arial, Courier, Times, Symbol)
Submit each figure as a separate file
images should be in tiff format
each figure should be supplied separately, and the figure captions should
be in a separate document
check to see that references are in correct format

Mining random . . task list

some reference information

Abstract


Main Ideas
Random peptides contain mimotopes of epitopes on real biological antigens
Specific random peptides can be used to isolate specific antibodies which
can further be verified with ELISA
There is a relationship between ELISA and array data
Best mimotopes are often good predicted B cell epitopes
Peptides bound on array can be organized into groups depending on the
mimotopes they contain

Experiments to Include
Array Data
Blocking Experiment
ELISA data of extracted SMC1fs with original protein
Bioinformatic process used (GEMODA, GLAM2, etc.) <- I may not want to include this paper anymore 01-02-2014d0950

Related Ideas or Further Experiments for Someone to Do
further experiment: test whether cancer patients have antibodies that
react more with the mimotopes or the original peptide

Key Peptide Sequences
TISKYVMVEPMRQHEEWGSC
AVSHQEMNEGEQGPMREGSC
RVGEMPMREYDISGGSGGSC
TAFYRTLTKHEVDPGIAGSC
WKPVPMRDFRTQPLMGDGSC
Human smc-1: TAIIGPNGSGCCGIYCHEEPQREDSSI
Mouse smc-1: TAIIGPNGSGCSGVYCHEEPQGEDSSV

Short-hand names
TISKY
AVSHQ
RVGEM
TAFYR

The AVLLM and ATK peptides are also used as negative controls

AVLLM is a mouse FS peptide

ATK is also a FS peptide found by MS
We probably do not need to mention the sources of these peptides in the
paper though.


Some Random Investigations and Notes 2-26-12


References 11-18-12

Some Other Notes
Word Document for Stephen's End of Year Summary
Using random peptides to identify and isolate specific antibodies
summary.doc
2nd version of Word Document
Using random peptides to identify and isolate specific antibodies summary
  1. doc
3rd version of Word Document
Using random peptides to identify and isolate specific antibodies summary
  1. doc
Powerpoint Presentation with figures from Shen
Using random peptides to identify and isolate specific antibodies figures
from Shen.ppt
Excel with one figure for SMC1fs antibody prevalence in samples
Prevalence of SMC1fs Antibodies.xls


===========================================================================
It looks like this paper may be written with Shen, Bart, and I. Here is
an initial outline with some main points and figures.
Using random peptides to identify and isolate specific antibodies
1-29-12.doc


===========================================================================
Actually, it looks like it will just be a paper between Shen and I

Notes from meeting with Kathy 2-15-12

Work on outline 2-26-12

Using random 2-26-12.docx

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

Meeting with Kathy about paper 3-6-12


===========================================================================
Work on paper
Mining Random Space for Real Antibody Epitopes 3-21-12.docx
"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\01-24-2014d0911\01-24-2014d0911\Mining Random Space for Real Antibody Epitopes 3-21-12.docx"

===========================================================================
figures for paper e-mail to shen 3-22-12
Work on paper
Mining Random Space for Real Antibody Epitopes 3-21-12.docx


===========================================================================
How many times does PQRE occur on array?


===========================================================================
Shen put some summary figures in this folder
S:\Research\Cancer_Eradication\Users\Shen\projects\SMC1A immune
signature\figs for paper
Here is a copy of those files with my modifications here
L:\storage\CIM Research Folder\DR\2012\5-3-12\figs from Shen


===========================================================================
52 peptide list can be found in Genespring under the Alta10K Genes->Gene
Lists->Kurt->Initial (Rabbit and some Mouse) SMC1 Immunosignatures->SMC1
temp Analysis with Phil on 5-6-10->SMC1 blocked and validated by
irrelevant and common to first blocking experiment

See 4-7-10 Powerpoint

Generation of 52 peptide list proceeded as follows (several filtering
steps were involved
"a-SMC1 blocked by SMC1 peptide exp. #2 (1:500, 11 steps)" list (491
peptides) was produced by determining which peptides decreased more than
two fold from SMC1 1:500 to 11 steps blocking (all data was normalized).
"a-SMC1 blocked by SMC1 peptide exp. #2 (1:500, 20 steps)" list (847
peptides) was produced by determining which peptides decreased more than
two fold from SMC1 1:500 to 20 steps blocking (all data was normalized).
"not blocked by SMC1 peptide" list (5685 peptides) was generated by
selecting peptides that differed from anti-SMC1fs 1:500 by at least 30%
"SMC1 blocked and validated by irrelevant" (222 peptides). Genes present
in a-SMC1 blocked by SMC1 peptide exp. #2 (1:500, 20 steps) and a-SMC1
blocked by SMC1 peptide exp. #2 (1:500, 11 steps), but not not blocked
by SMC1 peptide. The universe list was all genes.
"SMC1 blocked and validated by irrelevant and common to first blocking
experiment" (52 peptides). Genes present in a-SMC1 blocked by SMC1
peptide (blocked 11 steps in 3-11-10 experiment) and SMC1 blocked and
validated by irrelevant (generated combination list). The universe list
was all genes.


===========================================================================
I was trying to figure out how I once obtained a "182" peptides list, but
I was unable to find this.
Here's a brief analysis I attempted to do to get a similar list, but this
list had too many peptides (about 2000)
"F:\kurt\storage\CIM Research Folder\DR\2013\5-27-13\wiki_download\brief
analysis of smc1fs specific 5-4-12.xlsx"



===========================================================================
Finding peptides that increased in SMC1fs relative to naive 5-5-12


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

Some BLAST results of SMC1fs random peptide mimotopes 5-11-12


===========================================================================
Meeting with Kathy 7-24-12


===========================================================================
9-10-12

Shen was interested whether the PQRE or HEE motif was found in any of the
breast cancer peptides that Phil sent him. It looks like these motifs
were not found in very many of the peptides. Analysis found here:
C:\kurt\storage\CIM Research Folder\DR\2012\9-10-12\breast cancer peptide
analysis


===========================================================================
9-11-12

Worked on paper 9-11-12


===========================================================================
10-27-12 worked on paper

10-31-12 worked on paper


===========================================================================
Examples of short motifs or epitopes portal 11-4-12
52 peptide list can be found in Genespring under the Alta10K Genes->Gene
Lists->Kurt->Initial (Rabbit and some Mouse) SMC1 Immunosignatures->SMC1
temp Analysis with Phil on 5-6-10->SMC1 blocked and validated by
irrelevant and common to first blocking experiment





Some items