[RASMB] Time-stamp checks for SV data

[Judith Kornblatt]

Our upgrade was done in Oct 2012, version 5.8
Does anyone know if it also has this problem?
Judith Kornblatt
Concordia University
Montreal

On 1/25/2013 9:29 AM, Ghirlando, Rodolfo (NIH/NIDDK) [E] wrote:
>
> Dear friends and colleagues,
>
> 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).
>
> 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.
>
> In addition Beckman Coulter has been advised of this issue.
>
> Sincerely,
>
> Rodolfo Ghirlando
>
> FORWARDED MESSAGE
>
> Dear Colleagues,
>
> This is to let you know of a critical SEDFIT update with version 
> 14.0c, which you can download from 
> https://sedfitsedphat.nibib.nih.gov/software/Shared%20Documents/sedfit140c.zip
>
> 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.
>
> 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!
>
> 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.
>
> We have discussed this matter with our Beckman service engineer and it 
> appears as though the company is now addressing this issue.
>
> 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.
>
> Please let me know if you have any questions, or if any problems occur 
> with the new version.
>
> Best wishes and good luck,
>
> Peter
>
> Peter Schuck, PhD
>
> Chief, Dynamics of Macromolecular Assembly Section Laboratory of 
> Cellular Imaging and Macromolecular Biophysics National Institute of 
> Biomedical Imaging and Bioengineering, NIH
>
> 13 South Drive
>
> Bldg 13, Rm 3N17
>
> Bethesda, MD 20892
>
> phone: (301) 435-1950
>
> fax: (301) 480-1242
>
> email: schuckp at mail.nih.gov
>
>
>
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