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PEAKS

Identifies peptides from a sequence database with tandem mass spectrometry data. PEAKS employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve both the speed and accuracy of the database search. Each protein obtains a score by adding its three highest peptide CAA scores, and the protein feature of a peptide is the maximum score of the proteins containing this peptide. PEAKS also provides a user-friendly interface to show each resultant peptide spectrum match from de novo sequencing.

VIPER / Visual Inspection of Peak/Elution Relationships

Supports high-throughput peptide identification in the accurate mass and time (AMT) tag approach to high-throughput proteomics. VIPER combines into one software package a host of useful functions and capabilities that facilitate and standardize analysis and processing of liquid-chromatography-mass spectrometry (LC-MS) data for peptide quantitation and identification. This software uses a graphical user interface (GUI) generating 2D plots that display the monoisotopic masses observed in each mass spectrum.

Lutefisk

Allows de novo peptide sequence determinations from low-energy collision-induced dissociation (CID) data of tryptic peptides. Lutefisk is a program that rescores the final list of completed sequences using a combination of an ion intensity-based score plus a cross-correlation score. In addition to the mass spectral data, the software can incorporate other information into its sequence determinations (e.g. amino acid composition, peptide sequence tags and ambiguous or incomplete Edman sequencing data).

pSite

Permits amino acid confidence evaluation and modification site localization. pSite is based on a support vector machine (SVM) method to identify post-translational modifications and on a Bayesian model to evaluate the false amino-acid rate (FAR) at any given threshold. It follows five steps: (1) pre-processing tandem mass spectrometry (MS/MS) data, (2) enumerating the competitive sequences, (3) extracting features for each amino acid site, (4) estimating the confidence of each amino acid site, and (5) controlling the FAR of the reported amino acids.

NovoExD

Provides a de novo peptide sequencing method for ExD spectra. NovoExD is a modified spectrum graph with multiple edge types, denoted as graph with multiple edge types (GMET), derived from to model ExD spectra. It uses a spectrum graph model, considers multiple peptide tags to separate a peptide into small mass regions, and integrates fragment ion charge and amino acid composition (AAC) information. It then combines small regions to output complete sequences of candidate peptides.

SeqMS

Aids to the sequencing of peptides by interpreting mass spectra. SeqMS is designed to aid in de novo sequencing, which is based on high-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) spectra. The software permits the interpretation of other types of MS/MS data, such as those obtained via low energy CID-MS/MS and post-source decay (PSD) spectra of synthetic and proteolytic peptides. It should facilitate, in conjunction with high-quality data obtained with current high-performance MS, rapid and accurate sequencing of peptides.

NovoHCD

Combines amino acid combinations (AACs) and peptide tags to infer peptide sequences. NovoHCD uses a modified spectrum graph model with multiple types of edges for peptide sequencing. This method uses peptide tags to break the peptide sequencing problem into three parts: sequencing of tags, prefixes, and suffixes of the peptide. It then builds separate multi-edge graph models for each prefix and suffix, and AAC information is used to limit edges of each graph. It finally combines these three parts to output complete sequences of candidate peptides.

CycloBranch

A standalone, cross-platform and open-source de novo peptide identification engine for identification of nonribosomal peptides (NRPs) from MS/MS spectra. Currently, the identification of linear, cyclic, branched and branch-cyclic NRPs is supported. CycloBranch is based on a database of nonribosomal building blocks which currently contains 287 annotated monomers (521 monomers including isomers). When a building block is not present in a database or when a spectrum contains incomplete fragment ion series, peptide sequence tags are provided on the output. CycloBranch supports several file formats of peak lists (mzML and mzXML (requires OpenMS 1.11 installed), mgf (Mascot generic format), txt (containing a tab-separated m/z ratio and intensity on each line) and baf (a native file format of the manufacturer Bruker Daltonics; requires CompassX-Port 3.0 installed). CycloBranch can run in parallel on multiple threads and it has a graphical user interface.

pLabel

Allows peptide identification and spectral peaks labelling with corresponding fragment ions. pLabel aids users in manually validating peptide identifications via tandem mass spectrometry (MS/MS) through visualization of fragmentation patterns and representation of peptide-spectral match indices, and then to record these indices for the subsequent automatic validation by learning decision-tree model. The software also stores detailed fragmentation information for data mining to further deeply and quantitatively investigate the peptide fragmentation mechanisms.

MASIC / MS/MS Automated Selected Ion Chromatogram generator

Measures peptide abundances and Liquid Chromatography (LC) elution times in LC-Mass Spectrometry (MS)/MS analyses. MASIC uses an efficient processing algorithm to quickly generate mass specific selected ion chromatograms from a dataset and provides an interactive browser that allows users to examine individual chromatograms with a variety of options. The results can be visualized using MASIC Browser and are summarized numerically in text files. The abundance and elution time information computed for individual MS features enables more accurate generation of reference databases of mass and (elution) time tags as utilized by the AMT tag approach.

ACTG / Amino aCids To Genome

Obsolete
Maps peptides to genome, assuming all possible single exon skipping, junction variation allowing three edit distances from the original splice sites, exon extension and frame shift. ACTG provides a user friendly web interface. Users simply upload a peptide list and an optional variant call format (VCF) file if one wants to apply sample-specific point mutations to the splice graph before mapping peptides. Users can select a mapping method, a reference database to be used for filtering out known sequences, and what variations they consider. The output of the mapping can be downloaded from the web site.