Comparison of Proteomic, Metabolic, and Growth Profiles of Brettanomyces bruxellensis Isolates from Croatian Wines

Supplemental Table 1 Percentage of matched proteins for Brettanomyces bruxellensis wine isolates.

Supplemental Table 2  List of proteins expressed in the tested Brettanomyces bruxellensis isolates and the reference strain.

Supplemental Figure 1 MALDI-MS-MS spectra of the GIVGYTDEAVVSSDFITDTHSTIFDAK peptide in positive (upper) and negative (lower) ion mode (peptide m/z 3136.3286 in negative mass spectrometry (MS) of intact peptide after CAF-/CAF+ derivatization). The peptide was assigned according to the NCBI nr protein database for Dekkera/Brettanomyces bruxellensis. This figure has been added as a Microsoft PowerPoint file. In protein identification, only a perfect match was used for identification. A perfect match was achieved by positive- and negative-ion mode matching. Matching was achieved for a minimum of four amino acids in a row obtained in positive and negative MS-MS of the same peptide. 1.5% (12 proteins) of the total number of proteins were expressed in all data sets, which means that they could be used as biomarkers in Dekkera/B. bruxellensis yeast identification. Mismatch parameters are described in Butorac et al. (2016) and on the website http://rapidcell.proteinreader.com/maldi-msms-biotypization-protocol/.

Supplemental Figure 2 ProteinReader feature NCBI nr database match has been added as a Microsoft PowerPoint file. The CAF-/CAF+ method enables de novo sequencing of derivatized peptides with negative and positive-ion mode tandem mass spectrometry (MS-MS– and MS-MS+). Peptide sequences are read from MS-MS spectra and matched against those in the the entire NCBI nr database by a software named ProteinReader and confirmed by MS data of elucidated peptide mass sequences derived from the annotated genome. Matches for each peptide were sorted in the Dekkera/Brettanomyces bruxellensis subgroup of peptide hits.

• Supplemental_Data.pdf