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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 -"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\04-10-2014d1149 my revisions\SMC Mimotope Paper.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 01-05-2014d1213\Table 1.docx" -"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 01-05-2014d1213\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\figures for submission\figures 01-05-2014d1213\Supplementary Table 1.docx" -"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\figures for submission\figures 01-05-2014d1213\Supplementary Table 2.docx" -[location of data and files for figures for smc peptide paper 03-01-2015d2207] Version of document in which I had some notes for the sources of the figures -"D:\kurt\storage\CIM Research Folder\kwhittem\Papers\My Possible Papers\smc1\Mining Random Space for Real Antibody Epitopes2 5-4-12.docx" 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 -[Changes in peptide binding intensities following anti-SMCfs antibody depletion of serum] 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 -SPOT, SMC1A, SMC1Afs, KLH, PBST, BSA, HRP, TMB, SMCfs, TBST, PBS, TRIS Abbreviations listed in paper -BSA: Bovine serum albumin; HRP: Horse radish peroxidase; KLH: Keyhole limpet hemocyanin; PBS: Phosphate buffered saline; PBST: Phosphate buffered saline Tween-20; SMC1A: Structural maintenance chromosome 1A; SMC1Afs: Structural maintenance chromosome 1A frame-shift; SMCfs: A 17 amino acid SMC1A frameshift mutant; TBST: Tris Buffered Saline Tween-20; TMB: 3,3’,5,5’-Tetramethylbenzidine; TRIS: tris(hydroxymethyl)aminomethane 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 2.doc 3rd version of Word Document Using random peptides to identify and isolate specific antibodies summary 3.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 -sent email of data and files for figures; 03-01-2015d2231; email "raw data for figures" 3-1-15 https://mail.google.com/mail/u/0/#search/raw+data+for+figures/14bd7405d27677e8
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