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<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff
size=2>Chin,</FONT></SPAN></DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff size=2>First,
the proper statistical way to address any issue about whether a change in rms
residual is significant is to apply an F-test.</FONT></SPAN></DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff size=2>While
I would guess that you are indeed detecting sedimentation of a real low s
species, I think the question you should be asking yourself is whether the area
of that peak has any relevance for what you are trying to do. That is, this
material cannot possibly be your protein or a protein aggregate---most likely
you are detecting sedimentation of some buffer component. </FONT></SPAN></DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff size=2>If
this peak isn't due to protein, it shouldn't be counted in calculating fraction
main peak or any other property of the protein (for example weight-average
sedimentation coefficient), so why do you care whether its area is accurate?
Just copy the distribution table to another program and manually delete the low
s value region, or don't include it when you ask SEDFIT to integrate the
areas.</FONT></SPAN></DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff size=2>With
regard to the half-peak at s-max, that is quite different. The presence of
that half-peak probably indicates the presence of material sedimenting
faster than s-max, and there is no guarantee that the area of that half-peak
accurately measures the amount of such material. Thus if you want to
characterize all the aggregates in your sample then in my opinion you
really must raise s-max until you no longer see a half-peak at the upper
limit.</FONT></SPAN></DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff size=2>John
Philo</FONT></SPAN></DIV>
<DIV><SPAN class=865141415-01112004><FONT face=Arial color=#0000ff
size=2>Alliance Protein Laboratories</FONT></SPAN></DIV>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
rasmb-admin@server1.bbri.org [mailto:rasmb-admin@server1.bbri.org] <B>On
Behalf Of </B>Qin Zou<BR><B>Sent:</B> Thursday, October 28, 2004 5:41
AM<BR><B>To:</B> rasmb@server1.bbri.org<BR><B>Subject:</B> [RASMB] on low s
value peak in sedfit<BR><BR></FONT></DIV><BR><FONT face=sans-serif size=2>Dear
experts,</FONT> <BR><FONT face=sans-serif size=2>I have been reading some
discussions on low s value peaks using sedfit in this group. I have such a
partial peak with smin at 0.1s. I have tried Dr. Schuck's method that is to
increase s-min value gradually while monitoring the rmsd. Here is some of the
results:</FONT> <BR><FONT face=sans-serif size=2>s-min: 0.2s
0.5s 1.0s
1.2s
1.4s </FONT> <BR><FONT face=sans-serif
size=2>rmsd: 0.005249 0.0053
0.005556 0.005580
0.005588</FONT> <BR><BR><FONT face=sans-serif size=2>The height of the
partial peak did drop but never completely disappears. Couple of
questions:</FONT> <BR><FONT face=sans-serif size=2>1)Is the increase of the
rmsd shown above considered significant?</FONT> <BR><FONT face=sans-serif
size=2>2)If there is a sedimenting component at this low s, how do I integrate
this partial peak and the other complete peaks? It seems that moving around
s-min affects the integration alot. </FONT><BR><FONT face=sans-serif
size=2>3)There is also a little partial peak at s-max. If I only want to know
the loading percentage of all the aggregates, should I just integrate all the
way to the s-max?</FONT> <BR><BR><FONT face=sans-serif size=2>Thanks in
advance.</FONT> <BR><FONT face=sans-serif size=2>Regards,</FONT> <BR><BR><FONT
face=sans-serif size=2>Chin Zou</FONT></BLOCKQUOTE></BODY></HTML>