PubSpectra raw data that I had in my "to do" folder to add to the PubSpectra data set but never did.
PubSpectra has over 2000 spectra in it (last updated 2006) in Excel "big file" format - the XLSX file inside the zip file at
Anyone is welcome to add and organize new data yourselves. I used Un-Scan-It from Silk Scientific (www.silkscientific.com).
More importantly, I strongly adopting my PubSpectra format of 1 nm wavelength intervals, with the row number corresponding to nm. For example, 400 nm data appears in row 400.
Much of Urse Utzinger's "Spectra Arizona" data,
came from PubSpectra, through my collaboration with Carl Boswell (McNamara et al 2006 Cytometry), so please don't waste your time re-entering data Carl and Urs already have. On the other hand, Urs has added data to Spectra Arizona that would be nice to have in "1 nm step size" format in an Excel file.
See Urs posting to the confocal listserv on Sunday May 4, 2014 (and rest of that thread).
I encourage communicating any progress you make through the confocal listserv so that others do not duplicate your efforts. You are welcome to host your own additions to PubSpectra.
You can also obtain more data from
Chroma Spectra Viewer
and other web sites (many older filters from Semrock and Chroma and others are in Pubspectra).
Good luck obtaining fluorescent protein spectra numerical data from the researchers who have published. Roger Tsien and Robert Campbell supplied me many of the early FP spectra (mFruits, etc), but most researchers are unresponsive to sending spectra data (hence many PubSpectra data were generated by using Un-Scan-It on published graphs). The publishers are also at fault; they could request - maybe even require!!! - numeric data be provided for any publication.
Other things you could DO with fluorescence spectra data include (i) calculating the fluorescence spectral overlap integral ("J"), and fluorescence resonance energy transfer distances (FRET Ro) for all pairs of fluorophores, (ii) similarity matrix for all fluorophores (ex; Fluorescein vs Alexa Fluor 488 vs EGFP vs Venus YFP).
- fluorescence spectra,
Available at: http://works.bepress.com/gmcnamara/50/