Ortiz-Bermudez et 10.1073/pnas.0610074104.XXYYYYY103.

Supporting Information
Files in this Data Supplement: SI Figure 4 SI Figure 5 SI Methods

SI Fig. 4A SI Fig. 4B SI Fig. 4C Fig. 4. Assigned tandem mass spectra of five peptides generated by a trypsin digestion of Curvularia inaequalis chloroperoxidase that had been purified from colonized aspen meal. Fragment ions were manually assigned, and partial y- or bseries are shown.

Fig. 5. Sensitivity of the GC/MS method. The mass spectra shown are for uninoculated wood samples (A and C) and the least-chlorinated C. inaequaliscolonized wood sample, a 12-week aspen wafer (B and D), showing data obtained at the GC retention times of 5-chlorovanillin (A and B) and 2-chlorosyringaldehyde (C and D). 5-Chlorovanillin was found in the colonized wood [1.2 mg/g (dry weight)] but was undetectable in the uncolonized wood. Likewise, 2-chlorosyringaldehyde was found in the colonized wood [1.1 mg/g (dry weight)] but was undetectable in the uncolonized wood.

SI Methods Protein Identification and Sequencing.

In-gel digestions and mass spectrometric analyses were done at the Mass Spectrometry Facility of the Biotechnology Center, University of WisconsinMadison. Tryptic digests were analyzed by liquid chromatography/tandem mass spectrometry (LC-MS/MS) with an 1100 series LC/MSD Trap SL spectrometer (Agilent, Palo Alto, CA). LC of peptides before mass spectral analysis was done on a reverse-phase HPLC trap column (Zorbax 300SB-C18, 5-mm pores, 0.3-mm diameter 5 mm long, Agilent) followed by a reverse-phase separation column (Zorbax 300SB-C18, 3.5-mm pores, 0.075-mm diameter 150 mm long, Agilent), onto which 40 ml of each extracted peptide digest was automatically loaded. An Agilent 1100 series HPLC delivered solvents A [0.1% (vol/vol) formic acid/water] and B [95% (vol/vol) acetonitrile/0.1% (vol/vol) formic acid] at 10 ml/min to load the sample, followed by a flow rate of 0.28 ml/min to elute peptides directly into the nanoelectrospray over a 60-min gradient of 20-80% B. Peptides eluting from the HPLC column/electrospray source were trapped in an ion cell, and sequential MS/MS spectra spanning 300-2,200 m/z were generated for the five most abundant ions present at each switching event. Redundancy was limited by dynamic exclusion. MS/MS data were converted to matrix generic format files by using Agilent data analysis software. The resulting files were used to search the National Center for Biotechnology Information amino acid sequence database by using an in-house Mascot search engine (Matrix Science, London, U.K.) with methionines oxidized, cysteines carbamidomethylated, and glutamate and aspartate deamidated as variable modifications.