Spectra data for newest FPs

[F Javier Diez Guerra]

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Hi,

Looking for ex/em spectra data of several recent fluorescent proteins, I
find the nic.ucsf site (http://nic.ucsf.edu/FPvisualization/), an
excellent and updated tool, very useful for choosing among FPs, but no
spectra available. On the other hand, the spectra.arizona site
(http://www.spectra.arizona.edu/) offers several spectra but it is short
in FPs. Other sites maintained by several vendors (Omega, Life
Technologies, etc) are no better in this respect.

Any suggestions will be wellcome!

Thanks



--
Fco. Javier Diez-Guerra, PhD

Profesor Titular UAM
Servicio de Microscopía Confocal
Centro de Biologia Molecular Severo Ochoa
C/ Nicolás Cabrera, 1
Campus de Cantoblanco
28049 Madrid
SPAIN

Tel     [phone]
e-mail: [hidden email]

[George McNamara]

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Hi Javier,

I volunteer YOU to do the following:
* start digitizing your favorite spectra and posting them online, and
including them as numeric data in your manuscripts.
* encourage colleagues -- worldwide, not just your labmates -- to
include the spectra NUMERIC DATA, and extinction coefficients, quantum
yields, photodestruction rates, etc -- not just a thumbnail size and/or
overcrowded graph.
* when reviewing manuscripts for colleagues or journals, insist on
inclusion of all the data - spectra and otherwise - that went into the
manuscript. Decline to review for colleagues or journals that do not
include all data in the manuscript package or in a public data
repository (ex. PDB, GenBank, microarray data). Don't review manuscripts
that do not have a policy requiring all data be part of the manuscript.
* when editing -- especially if you are editor in chief of eLife, or the
'CNS' journals -- , insist on inclusion of all the data - spectra and
otherwise - that went into the manuscript. Decline any manuscripts that
do not include all the data in the manuscript package or in a public
data repository.

In the past couple of years there has been more interest in
reproducibility and replication in science. Having all the data -
whether it is the photon counts from Eric Betzig's latest lattice light
sheet microscopy paper, or the original Stefan Hell STED paper - would
help everyone move science forward.

//

With respect to Urs Utzinger's http://www.spectra.arizona.edu this is
the 3rd iteration of Carl Boswell's spectra graphing project. Carl and I
published on the 2nd iteration in Cytometry in 2006 - that PDF, and my
equally awesome review with Yuval Garini and Ted Young, and all the data
is available in the PubSpectra XLSX Microsoft Excel 'big data' format
file inside the zip download at

http://works.bepress.com/gmcnamara/9/

The PubSpectra XLSX file gives credit to the sources of every spectral
trace in the dataset. Robert Campbell and Roger Tsien sent me a lot of
the early FP spectra. I digitized a lot of published graph traces using
Silk Scientific's Un-Scan-It, you and/or others are welcome to getting
the 2006 and later FPs digitized and organized into a standard format.
As I point out in our 2006 Cytometry PubSpectra discussion, data is not
subject to copyright (at least in the U.S.) -- please digitize, organize
and post.

//

With respect to current graphing sites, I usually use Semrock
SearchLight for comparing spectra.
http://searchlight.semrock.com/
This is partly because it has spectra data for some of the hardware in
the microscope in my (Prof. Laurence Cooper's) lab here at MD Anderson
Cancer Center:
Lumencor SOLA (early serial number - Tom DiMatteo,
http://www.epitechnology.com/ , explained to me early SOLA's have single
LED capability - now working in MetaMorph 7.8.8)
Several Semrock single exciter filters in an ASI wheel
Semrock LED-Quad (D/F/R/Cy5) and Triple (Cyan/Yellow/HcRed) filter cubes

As for me, I have a lot of serial killing movies to make - this
http://www.jove.com/video/50058/quantitative-high-throughput-single-cell-cytotoxicity-assay-for-t
was done before I moved to Houston, and still have not made any
Tattletales,
http://works.bepress.com/gmcnamara/42
http://works.bepress.com/gmcnamara/63
in our lab. Of course by waiting, we now have better fluorescent
proteins -- EGFP is so 1996
(http://www.ncbi.nlm.nih.gov/pubmed/8885998)vs mNeonGreen, the current
brightest monomer, http://nic.ucsf.edu/FPvisualization/ Stokes Shift vs
Brightness
and others have validated my binary Tattletales concept (see "63" page).

Sincerely,

George


On 11/21/2014 8:28 AM, "Fco. Javier Díez Guerra" wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi,
>
> Looking for ex/em spectra data of several recent fluorescent proteins,
> I find the nic.ucsf site (http://nic.ucsf.edu/FPvisualization/), an
> excellent and updated tool, very useful for choosing among FPs, but no
> spectra available. On the other hand, the spectra.arizona site
> (http://www.spectra.arizona.edu/) offers several spectra but it is
> short in FPs. Other sites maintained by several vendors (Omega, Life
> Technologies, etc) are no better in this respect.
>
> Any suggestions will be wellcome!
>
> Thanks
>
>
>

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales http://works.bepress.com/gmcnamara/42