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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D">Dear Rodolfo, Dear Peter,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D">Thanks a lot for the information and the subsequent implementation of the correction in SEDFIT. We very recently (Jan 2013) acquired a Beckman XL-I with software
version 6 and the S-values and MW of well-known molecules were indeed ~10% higher than measured previously with older machines when I was at university. I loaded our experiments performed with the new machine/software until now in SEDFIT and it diagnosed 10.4
% time stamp error. Analysis of the corrected files yielded the familiar values for S and MWG. I also looked in the header of the first interference scan immediately after the machine reached the desired speed (42 000). With identical settings, the old version
stamps the scan with 154 seconds, the new version 6 software with 163 seconds. I will also monitor the time needed for acceleration to 42 000 and 50 000 rpm (we only have a TI50 so far) as Borries mentioned.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D">Kind regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D">Alexander
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Dr. Alexander Bepperling</span></b><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Scientist
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Biophysical Characterization<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">HEXAL AG<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Keltenring 1 + 3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">D-82041 Oberhaching<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">GERMANY<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Phone +49 89 613670248<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Fax +49 89 613670147<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D"><a href="mailto:alexander.bepperling@sandoz.com"><span style="color:blue">alexander.bepperling@sandoz.com</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D"><a href="http://www.hexal.de/"><span style="color:blue">www.hexal.de</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Hexal AG Sitz der Gesellschaft: Holzkirchen<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Amtsgericht: München HRB-Nr. 110375<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D">Vertretungsberechtigt: Hans-Helmut Fabry, Karl-Heinz Marx, Isabell Remus, Wolfgang Späth, Dieter Ziebold<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> rasmb-bounces@list.rasmb.org [mailto:rasmb-bounces@list.rasmb.org]
<b>On Behalf Of </b>Ghirlando, Rodolfo (NIH/NIDDK) [E]<br>
<b>Sent:</b> Freitag, 25. Januar 2013 15:30<br>
<b>To:</b> rasmb@list.rasmb.org<br>
<b>Subject:</b> [RASMB] Time-stamp checks for SV data<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Dear friends and colleagues,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">It has come to our (Joy Zhao, Peter Schuck, Grzegorz Piszczek, Chad Brautigam and myself) attention that sedimentation coefficients based on SV data collected
using the ProteomeLab XLA/I version 6 acquisition software are up to 10% larger than expected (depending on the rotor speed).<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">We have traced this to a smaller than expected elapsed time stamp in the file header. A correction for this has been implemented in SEDFIT based in part
on the Windows OS file creation time stamp. This version has been released, as indicated in the forwarded email from the SEDFIT-L list below, and we will report more details on this shortly.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">In addition Beckman Coulter has been advised of this issue.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Sincerely,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Rodolfo Ghirlando<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">FORWARDED MESSAGE<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Dear Colleagues,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">This is to let you know of a critical SEDFIT update with version 14.0c, which you can download from
<a href="https://sedfitsedphat.nibib.nih.gov/software/Shared%20Documents/sedfit140c.zip">
https://sedfitsedphat.nibib.nih.gov/software/Shared%20Documents/sedfit140c.zip</a><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">It has a very important new feature for the analysis of sedimentation velocity: it automatically compares the elapsed times reported in the data file headers
with the time differences obtained from the file creation timestamps generated by the Windows operating system on the PC.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Why would we need this? In the course of a joint study between our lab and the labs of Rodolfo Ghirlando, Greg Piszczek and Chad Brautigam, we have recently
discovered that data files can have elapsed time entries less than the differences from the operating system timestamp, by as much as 10%. Obviously, if the elapsed time entry is 10% too low then this leads to s-values that are 10% too high!<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">We have double checked data from many different instruments, and correlated this discrepancy in elapsed times with the ProteomeLab data acquisition software
version 6. No time differences, or only trivial ones, were observed for instruments running earlier versions of the data acquisition software. In some runs the overall difference amounts to hours at the end of the run, and I believe that the operating system
timestamp is correct. We will distribute more detailed information shortly, but want to give you already a heads-up in the meantime with this note: If you are running version 6 you may want to examine the data files, and/or time the data acquisition process
yourself, to verify.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">We have discussed this matter with our Beckman service engineer and it appears as though the company is now addressing this issue.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">The new SEDFIT release can fix this problem for the data analysis. First, it automatically checks and creates a report if a systematic and significant
discrepancy exists between differences in the file time-stamp and differences in the header elapsed time. If there appears to be a problem (i.e. apparent dilation factor greater than a user-defined threshold, initially defaulted to 1.005 or 0.5%), SEDFIT will
create a report and then offer to write data files (under different names, of course) with time entries based on a dilation factor extracted from the file timestamps. Subsequent analysis of these time-corrected data files should eliminate the problem, as it
did perfectly for the data in our study. Such time-corrected scan files should also be the ones loaded into SEDPHAT, which will get its own update shortly.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Please let me know if you have any questions, or if any problems occur with the new version.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Best wishes and good luck,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Peter<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Peter Schuck, PhD<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Chief, Dynamics of Macromolecular Assembly Section Laboratory of Cellular Imaging and Macromolecular Biophysics National Institute of Biomedical Imaging
and Bioengineering, NIH<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">13 South Drive<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Bldg 13, Rm 3N17<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">Bethesda, MD 20892<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">phone: (301) 435-1950<o:p></o:p></span></p>
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<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New"">email:
<a href="mailto:schuckp@mail.nih.gov">schuckp@mail.nih.gov</a> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
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