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Sensitive identification of phosphopeptides in brain tissue using Ettan MDLC and Finnigan LTQ

linear salt gradient (A: 20 mM citric acid, 25% CH3CN; B: A+ 1 M NH4Cl) where fractions were collected twice every minute (Fig 1). The fractions were injected onto a 0.3 ×5 mm RPC trap column (Zorbax™, Agilent), where they were desalted. RPC separation was performed on a 0.075 ×150 mm analytical column (Zorbax, Agilent) with a 50-min linear gradient (A: 0.1% formic acid; B: 84% CH3CN and 0.1% formic acid). To increase throughput, one pair of columns was equilibrated while the other pair was used for analysis.

Mass spectrometry
A Finnigan LTQ linear ion trap was used (Thermo Electron). The MS method consisted of a cycle combining one full MS scan with three MS/MS events (25% collision energy) followed by an MS3 event (35% collision energy) that was triggered upon detection of -98, -49, or -32.7 Da from the precursor (neutral loss of phosphoric acid, charge states 1+, 2+, and 3+). Dynamic exclusion duration was set to 30 s. The MS/MS and MS3 spectra from all the runs were searched using TurboSEQUEST™ protein identification software (Thermo Electron). Modifications were set to allow for the detection of oxidized Met (+16); carboxyamidomethylated Cys (+57); phosphorylated Ser, Thr, and Tyr (+80); and dehydrated Ser and Thr (-18).


Results and discussion
By injecting a large amount of sample and separating it on an analytical scale SCX column, collecting the fractions, and then injecting these onto a nanoscale LC, the peptides of low abundance, such as phosphopeptides, could be detected (3). Thirty fractions were analyzed—one example showing the chromatogram and the MS3 events from one of the fractions is shown in Figure 2. Phosphopeptides were found in one third of the analyzed SCX fractions, mainly eluting at the beginning of the salt gradient.
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