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Gabriels, R.

Publications and source records attributed to Gabriels, R..

2 recordsLinked to original sources
bioRxiv2019

COSS: A fast and user-friendly tool for spectral library searching

Spectral similarity searching to identify peptide-derived MS/MS spectra is a promising technique, and different spectrum similarity search tools have therefore been developed. Each of these tools, however, comes with some limitations, mainly due to low processing speed and issues with handling large databases. Furthermore, the number of spectral data formats supported is typically limited, which also creates a threshold to adoption. We have therefore developed COSS (CompOmics Spectral Searching), a new and user-friendly spectral library search tool that relies on a probabilistic scoring function, and that includes decoy spectra generation for result validation. We have benchmarked COSS on three different spectral libraries and compared the results with established spectral search and sequence database search tools. Our comparison showed that COSS identifies more peptides, and is faster than other tools. COSS binaries and source code can be freely downloaded from https://github.com/compomics/COSS. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/640458v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1b1bfacorg.highwire.dtl.DTLVardef@9ec990org.highwire.dtl.DTLVardef@c31055org.highwire.dtl.DTLVardef@654e47_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗
bioRxiv2019

Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

MS2PIP is a data-driven tool that accurately predicts peak intensities for a given peptides fragmentation mass spectrum. Since the release of the MS2PIP web server in 2015, we have brought significant updates to both the tool and the web server. Next to the original models for CID and HCD fragmentation, we have added specific models for the TripleTOF 5600+ mass spectrometer, for TMT-labeled peptides, for iTRAQ-labeled peptides and for iTRAQ-labeled phosphopeptides. Because the fragmentation pattern is heavily altered in each of these cases, these additional models greatly improve the prediction accuracy for their corresponding data types. We have also substantially reduced the computational resources required to run MS2PIP, and have completely rebuilt the web server, which now allows predictions of up to 100.000 peptide sequences in a single request. The MS2PIP web server is freely available at https://iomics.ugent.be/ms2pip/.

bioinformatics↗