Using+random+peptides+to+identify+and+isolate+specific+antibodies+Paper

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
 * Title of Paper**: Using random peptides to identify and isolate specific antibodies

aka smc paper with kathy and shen

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

most recent version of paper "C:\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\12-30-12 revision\SMC1Afs_Mimotopes 12-30-12 by kurt.docx"

most recent version of figures "C:\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 12-30-12\figures short names\All Figures 12-30-12.pdf"

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**

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
 * Main Ideas**

Array Data Blocking Experiment ELISA data of extracted SMC1fs with original protein Bioinformatic process used (GEMODA, GLAM2, etc.)
 * Experiments to Include**

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

TISKYVMVEPMRQHEEWGSC AVSHQEMNEGEQGPMREGSC RVGEMPMREYDISGGSGGSC TAFYRTLTKHEVDPGIAGSC WKPVPMRDFRTQPLMGDGSC Human smc-1: TAIIGPNGSG CCGIYCHEEPQREDSSI Mouse smc-1: TAIIGPNGSG CSGVYCHEEPQGEDSSV
 * Key Peptide Sequences**

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

Word Document for Stephen's End of Year Summary 2nd version of Word Document 3rd version of Word Document Powerpoint Presentation with figures from Shen Excel with one figure for SMC1fs antibody prevalence in samples
 * Some Other Notes**

It looks like this paper may be written with Shen, Bart, and I. Here is an initial outline with some main points and figures.

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



Meeting with Kathy about paper 3-6-12

Work on paper

figures for paper e-mail to shen 3-22-12 Work on paper

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