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2 protocols using maldi target plate

1

MALDI-TOF/TOF Protein Identification

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Protein samples were loaded into BoltTM 4–12% Bis-Tris Plus gradient gel (Invitrogen), and the target protein gel band was excised and digested with trypsin as described40 (link). After cleanup steps using C18 ZipTips (Millipore), the samples were mixed with an equal amount of matrix solution containing 10 mg/ml R-cyano-4-hydroxycinnamic acid in 0.1% TFA/50% ACN and spotted onto a 384-well stainless steel MALDI target plate (Applied Biosystems, Foster City, CA). An ABI 4800 Proteomics Analyzer MALDI TOF/TOF mass spectrometer (Applied Biosystems) was used to analyze the samples. For protein ID, combined MS and MS/MS data were submitted via GPS Explorer (version 3.6, Applied Biosystems) to Mascot server (version 2.0, Matrix Science). The swissprot database (including 545536 sequences, 194023197 residues) was utilized for the search.
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2

Elemental Analysis and MALDI-TOF-MS of Humic Substances

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Elemental analysis was performed on freeze-dried samples of HS (5 mg) by using Vario EL cube (Elementar Analysensysteme GmbH, Germany). The solid-state 13 C-NMR was performed on a Bruker AVANCE III 400WB spectrometer. MALDI had the advantage of forming singly charged ions. Combined with TOFMS, it could detect the absolute MW of HS rather than the apparent MW detected in high performance size exclusion chromatography [39] . In details, the HS samples were dissolved in 50% acetonitrile (ACN) and 0.1% trifluoroacetic acid (TFA), then mixed with same amount of matrix solution containing 10 mg/mL of α-cyano-4-hydroxycinnamic acid (CHCA) in 0.1%TFA-50%ACN, and spotted onto a 384-well stainless-steel MALDI target plate (Applied Biosystems, USA). An ABI 4800 MALDI TOF/TOF mass spectrometer (Applied Biosystems, USA) was used to analyze the samples on the MALDI target plates. For MS analyses, typically 1600 shots were accumulated for each sample. The MALDI spectra of HS in current study were consistently found to contain a number of common peaks. It was difficult to assign the origins to peaks in the low m/z range, as they could be attributed to matrices, contaminants or HS fragments during ionization. Thus only the largest m/z peak with signal-to-noise ratio over 3 in each spectrum, which was more likely associated with the ionized HS molecule, was reported in this work.
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