[RASMB] Time-stamp checks for SV data

[John Burgner]

Taking any large time interval from a series of scans and calculating the
w^2dt for that interval gives the same value calculated from the w^2t values
in the file header so yes both values are incorrect.  Note also that windows
stores file creation times accurate to 1 sec. 
John Burgner

-----Original Message-----
From: rasmb-bounces at list.rasmb.org [mailto:rasmb-bounces at list.rasmb.org] On
Behalf Of Walter Stafford
Sent: Friday, January 25, 2013 10:38 AM
To: Borries Demeler
Cc: rasmb at list.rasmb.org
Subject: Re: [RASMB] Time-stamp checks for SV data

Borries,

	The time values in the file header are "elapsed time" from the the
time the rotor starts turning and should not be used in analysis in any
case. SEDANAL uses integral(w^2 dt), which is the correct value to use for
all analyses. 

So your question is important: Are those values reported correctly or not in
version 6?

Walter

_________________________
Walter Stafford
wstafford3 at walterstafford.com



_________________________
Walter Stafford
wstafford3 at walterstafford.com



On Jan 25, 2013, at 10:13, Borries Demeler wrote:

> Rodolfo:
> 
> are w^2t values reported in the file header not affected, or has that 
> not been investigated? I do not have this version to test myself, but 
> such errors would propagate into some analysis methods in UltraScan as 
> well. As far as I know the w^2t values are reported directly from the 
> DA system of the XLA, I am not certain where the time values 
> originate. The w^2t values *may* be affected as well, and that should be
looked at by someone with a Proteomelab ver.6.
> 
> -borries
> 
> 
> On Fri, Jan 25, 2013 at 09:29:39AM -0500, 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/sedfi
>> t140c.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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