#Universal database tool software

linear ion-trap), вЂHighвЂ™ indicates high-resolution instruments (e.g. вЂLowвЂ™ in Instrument indicates low-resolution instruments (e.g. Spectral types are represented as paths in the graph representing possible choices of the fragment method (Fragmentation), the instrument measuring product ion m/z (Instrument), the protocol used to prepare a sample (Protocol), and the enzyme used to digest proteins (Enzyme). We emphasize that although MS-GF+ is not specifically designed for any particular experimental set-up, it improves on the performance of tools specifically designed for these applications (for example, specialized tools for phosphoproteomics).

For all these data sets, MS-GF+ significantly increases the number of identified peptides compared with commonly used methods for peptide identifications. We benchmark MS-GF+ using diverse spectral data sets: (i) spectra of varying fragmentation methods (ii) spectra of multiple enzyme digests (iii) spectra of phosphorylated peptides and (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).

#Universal database tool software

Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but the software tools to analyse tandem mass spectra are lagging behind.