Mass Error Calculated Incorrectly

[Nick]

The mass error in ppm calculation is and has been completely wrong in
the last several version. We've sent in requests to have it fixed but
so far nothing. Might we see some action on this soon....

[Jason]

This is an error we are looking into. We will keep you posted on our
progress.

[Nick]

It's been about a month since the last time we reported this error and
longer since it has been present. Are we close to getting a fix? My
customers are annoyed to say the least.

Nick

> > so far nothing.  Might we see some action on this soon....- Hide quoted text -
>
> - Show quoted text -

[Jason]

Hello Nick,

We have fixed this error in the latest release of Scaffold which
should be on the web later today. The error was caused by misreading
the search type (average or monoisotopic) in SEQUEST *.srf files. Let
us know if you have any other questions.

Jason

[Edina Csaszar]

Dear Jason,
Is there a possibility to have a list of overlapping and unique
proteins from two replicates? I would practically need the
"background" info to the protein Venn diagramms.
Best regards: Edina

Edina Csaszar PhD
Max F. Perutz Laboratories
Dept. of Biochemistry
Mass Spectrometry Facility
Dr. Bohr-Gasse 3
A-1030 Vienna
phone: +43 (0) 664 60277 74891
fax:+43 1 79044 110

http://www.projects.mfpl.ac.at/msfacility/

[Jason]

Hello Edina,

There is not a way to view overlapping and unique proteins between
multiple biosamples in Scaffold's Venn Diagrams at this time. You can
see this information in Scaffold's Samples view. I would suggest doing
a Samples view export to Excel, and then creating a pie chart or venn
diagram in Excel using that export. It should be a very quick process,
and it allows you to get at the shared and unique protein information.
Please let me know if this option does not work for you.

Jason

[Hammer]

Hello Jason,

I have two things I want to ask you, because we have problems with our
Scaffold 2.103, running on our 64 Bit operating system:

We have several sets of samples to analyze which include 20 or 24 samples
with 1.2-1.5. GB each in size. Already setting up the analysis takes a long
time (loading per file from 8 min to 20 min) accompanied also by error
messages (see attached log.file). Furthermore, one sample set could not be
analysed at all (we tried it multiple times) giving a error message. The
corresponding log files are attached to this e-mail.

We looked for updates which help to improve the performance of Scaffold and
found upgrade 2.2. Does our license cover the use of this upgrade? If so,
does there exist also a Batch version of this upgrade which can be installed
on the Sorcerer?

Thanks for help in advance

Elke