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Mass spectrometry analysis and data processing

YS Yuehong Shen
PL Pengfei Liu
TJ Taolue Jiang
YH Yu Hu
FA Franco K. C. Au
RQ Robert Z. Qi
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γTuRCs were isolated by anti-FLAG immunoprecipitation as described above and without streptavidin pulldown. After anti-FLAG immunoprecipitation, bound proteins were eluted by incubating the beads with FLAG peptide (200 ng μl−1)17, 19 and the eluted proteins were resolved using SDS-PAGE and stained with SYPRO Ruby (Thermo Fisher Scientific). Protein bands excised from the SDS-PAGE gels were digested with trypsin, and the extracted peptides were analyzed using mass spectrometry (LTQ Velos linear ion-trap LC–MS system, Thermo Fisher Scientific). The acquired tandem mass spectra were subject to gene database searches by using the MASCOT search engine (Matrix Science).

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