While trypsin remains a dominant protease in proteomics studies, digesting proteins with diverse proteases is becoming popular. New fragmentation technologies have emerged and high-precision mass spectrometers like Orbitrap have become widely available. Mass spectrometry (MS) instruments and experimental protocols have greatly advanced over the last decade. We emphasize that while MS-GF+ is not specifically designed for any particular experimental set-up, it improves upon the performance of tools specifically designed for these applications (e.g., specialized tools for phosphoproteomics). For all these datasets, MS-GF+ significantly increases the number of identified peptides compared to commonly used methods for peptide identifications. We benchmark MS-GF+ using diverse spectral datasets: (i) spectra of varying fragmentation methods (ii) spectra of multiple enzyme digests (iii) spectra of phosphorylated peptides (iv) spectra of peptides with unusual fragmentation propensities produced by a novel alpha-lytic protease. We present a database search tool MS-GF+ that is sensitive (it identifies more peptides than most other database search tools) and universal (it works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols). Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but the software tools to analyze tandem mass spectra are lagging behind.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |