Enhancing Peptide Identification by Combining an Efficient Protein Extraction Procedure with Dynamic Inclusion/Exclusion Lists in Data-Dependent LC-MS/MS Acquisition Mode

摘要

1) With the optimized sample preparation procedure (i.e. M1_P3 protocol), we were able to significantly improve the solubilization of both total proteins, and in particular of hydrophobic proteins, from MDDCs cellular extracts. This resulted in an average increase of 15% in the total protein identifications. 2) The use of exclusion/inclusion lists during MS data-dependent acquisition increases both peptide and total protein identifications, therefore improving the proteome coverage of MDDC samples. Furthermore, this data acquisition strategy allows the use of fewer numbers of dependent scans and longer accumulation times further improving protein identification. 3) The increase of the duration of the LC gradient does not correlate with a measurable improvement in protein identification