See us at ABRF - as if you didn't already know

[mpitman]

We're in booth 305, which I think is semi-close to the entrance.

Cheers,

Mark P.

[Dobrowsky, Rick Thomas]

Dear All,

Scaffold 2 is aggravatingly slow on my newer desktop even using a small
1000 protein data set. Is anyone else experiencing the same?

Rick T. Dobrowsky, Ph.D.
Professor
Department of Pharmacology and Toxicology
University of Kansas
5064 Malott Hall
1251 Wescoe Hall Dr.
Lawrence, KS 66045-2505

phone 785-864-3531
fax 785-864-5219

[Jason]

Hello Dr. Dobrowsky,

Scaffold 2.0 will load data somewhat more slowly than Scaffold 1.7.
This is due to the increased processing for things like the
Similarities view. Scaffold 2.0 should not be incredibly slow compared
to Scaffold 1.7, especially when loading a small 1000 protein
dataset.

Could you tell me how many spectra are in your 1000 protein dataset,
and how large are (in MB) the file(s) being loaded.

Thanks,

Jason

[Dobrowsky, Rick Thomas]

Jason,

Thanks for the quick reply. I was comparing three data sets each of
about 22K-26K in total spectra. On my computer, the program boots up
rather slowly but loads the data at a rate pretty similar to v1.7. What
has been bogging down is the switch between the sample window and the
new quantitation window. It seems to take 30-60 sec to switch screens.
However, staying within the quantitation window and using the pull down
menu to switch proteins, results in a new spectral count graph rather
quickly. Exporting the spectrum report data to Excel was really slow. I
just started trying the new version since I'm really attracted to the
quantitative ability. We have been doing SILAC but I would like to
compare results from real tissues. I'm trying to determine how well and
reliably Scaffold can do this.

Rick

[Dobrowsky, Rick Thomas]

Sorry, forgot to tell you the file was about 73 MB

[mpitman]

Hi Rick,

After running through multiple sets of data are you experiencing the
same slowness consistently, or does it happen on some data and not
others? If it's only intermittent, can you think of anything that is
shared by those files which are slow.?

Mark P.