For top-down protein database search and identification from tandem mass 
spectra, our isotopic envelope fingerprinting search algorithm and ProteinGoggle 
search engine have demonstrated their strength of efficiently resolving heavily 
overlapping data as well separating non-ideal data with non-ideal isotopic 
envelopes from ideal ones with ideal isotopic envelopes. Here we report our 
updated ProteinGoggle 2.0 for intact protein database search with full-capacity. 
The indispensable updates include users' optional definition of dynamic 
post-translational modifications and static chemical labeling during database 
creation, comprehensive dissociation methods and ion series, as well as a 
Proteoform Score for each proteoform. ProteinGoggle has previously been 
benchmarked with both collision-based dissociation (CID, HCD) and electron-based 
dissociation (ETD) data of either intact proteins or intact proteomes. Here we 
report our further benchmarking of the new version of ProteinGoggle with 
publically available photon-based dissociation (UVPD) data 
(http://hdl.handle.net/2022/17316) of intact E. coli ribosomal proteins.
BIOLOGICAL SIGNIFICANCE: Protein species (aka proteoforms) function at their 
molecular level, and diverse structures and biological roles of every proteoform 
come from often co-occurring proteolysis, amino acid variation and 
post-translational modifications. Complete and high-throughput capture of this 
combinatorial information of proteoforms has become possible in evolving 
top-down proteomics; yet, various methods and technologies, especially database 
search and bioinformatics identification tools, in the top-down pipeline are 
still in their infancy stages and demand intensive research and development.