A thorough DB search engine comparison for UDMS~E data has been performed for first time. State-of-the-art peptide-centric MS/MS database search engines can process HDMS~E/UDMS~E peptidomics data, enhancing DIA identification performance for phosphopeptide samples.Pedro Navarro...
De novo sequencing derives the peptide sequence directly from the MS/MS spectrum, whereas a database search queries a sequence database for the best peptide to explain the peaks in the MS/MS spectrum. Representative de novo sequencing software packages include PEAKS (1), PepNovo (2), NovoHMM...
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFragger. Here, we present a new tool, MSBooster, for ...
The database has a web-based user interface with a simple, Google-like search function, advanced text search, and BLAST and Smith-Waterman search capabilities. The major source of peptide sequence data comes from text mining of MEDLINE abstracts. Another component of the database is the peptide...
MS-GF + 27, which is an open-source database search tool integrated in Glyco-Decipher, is then used to search for the resulting spectra in proteome databases for the initial identification of peptide backbones. For a second-stage search, the fragmentation patterns of each peptide backbone...
Users can click on the Database icon and the search interface appears. APD can then be searched in multiple ways. As a dictionary, the user can ®nd out whether a speci®c peptide is collected in APD by entering the peptide name or the ...
and they encouraged researchers to use multiple databases and annotation tools [105]. Xiao et al. proposed a metagenomic taxonomy-guided database-search strategy (MT) and found that peptides detected by MT were 1.7 fold more than those via using a standard metagenomic database in human stool ...
The database update is semi-automated with human checking and verification of the data to ensure the correctness of the data stored. The latest release SPdb release 3.2 contains 18,146 entries of which 2,584 entries are experimentally verified signal sequences; the remaining 15,562 entries are ...
vitripennis AMP repertoire, we employed three complementary approaches to database search of the N. vitripennis genome (see additional file 1). Firstly, we chose A. mellifera AMPs (e.g. mellitin, apidaecin, apisimin, abaecin, hymenoptaecin, defensins) as queries to recognize their ...
Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to ...