[RASMB] Time-stamp checks for SV data

[Bepperling, Alexander]

Dear Rodolfo, Dear Peter,

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.

Kind regards

Alexander


Dr. Alexander Bepperling
Scientist
Biophysical Characterization
HEXAL AG
Keltenring 1 + 3
D-82041 Oberhaching
GERMANY

Phone    +49 89 613670248
Fax         +49 89 613670147
alexander.bepperling at sandoz.com<mailto:alexander.bepperling at sandoz.com>
www.hexal.de<http://www.hexal.de/>
Hexal AG Sitz der Gesellschaft: Holzkirchen
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From: rasmb-bounces at list.rasmb.org [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of Ghirlando, Rodolfo (NIH/NIDDK) [E]
Sent: Freitag, 25. Januar 2013 15:30
To: rasmb at list.rasmb.org
Subject: [RASMB] Time-stamp checks for SV data

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<mailto:schuckp at mail.nih.gov>


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