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MSPLIT-DIA / Mixture-Spectrum Partitioning using Libraries of Identified Tandem mass spectra

Permits untargeted and sensitive peptide identification in data-independent acquisition (DIA) data. MSPLIT-DIA is a spectral matching tool that uses spectrum projections to match library spectra to each DIA spectrum. This method also evaluates the similarity of the matched peaks between library spectra and multiplexed spectra across multiple consecutive DIA spectra. Assay libraries for targeted extraction tools are automatically generated by MSPLIT-DIA to facilitate coupling of sensitive identification with accurate quantification from DIA data.

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.

BiblioSpec

Permits to create and search spectrum libraries. BiblioSpec is a flexible spectrum comparison program that could be used in other applications such as for rapid detection of specific peptides of interest, for finding spectra in common between two experiments. It consists of several independent programs. The three mains are (i) BlibBuild, which creates a spectral library of mass spectra, (ii) BlibFilter, which modifies an existing spectrum library to contain only one spectrum per peptide, and (iii) BlibSearch, which matches query spectra to library spectra.

xiFDR

Analyzes the results of user’s preferred cross-link search engine. xiFDR is a search-tool-independent application that supports two modes of operation for cross-links: directional and nondirectional. The application also maximizes the number of returned hits for a desired false discovery rate (FDR). xiFDR applies a stepwise FDR: it first filters the peptide-spectrum matches (PSMs) to a specified FDR and then aggregates the PSMs to unique combinations of peptide pairs, classifies these again by an FDR and accumulates the peptide pairs that pass the FDR to unique residue pairs.

SEQUEST

Associates uninterpreted tandem mass spectra of peptides with amino acid sequences (AAS). SEQUEST uses fragmentation patterns in tandem mass spectra to detect AAS from protein and nucleotide database. It correlates the spectrum with the experimental data via the prediction of fragment ions of an AAS. This software allows database searches with experimental data directly and offers to users the ability to correlate exactly uninterpreted tandem mass spectra to sequences to the database.

rTANDEM

Interfaces the X!Tandem protein identification algorithm. rTANDEM can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. This brings to proteomics the many advantages of building an analysis pipeline in the R/Bioconductor statistical platform: easy deployment on high-performance computing and cloud computing through Bioconductor Cloud Amazon Machine Image (AMI), fully open-source workflows, interconnectivity of annotation and analytic packages, full reproducibility of analysis, etc.

PEAKS DB

Identifies peptides from a sequence database with tandem mass spectrometry (MS/MS) data. PEAKS DB 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. The net outcome is an increase in both sensitivity and accuracy and an overall superior performance to other commonly used search engines. This package is a particularly useful tool for identifying peptides with post-translational modifications (PTMs).

MS-GFDB

A database search tool based on MS-GF. MS-GFDB outperforms Mascot for ETD spectra or peptides digested with Lys-N. For example, in the case of ETD spectra, the number of tryptic and Lys-N peptides identified by MS-GFDB increased by a factor of 2.7 and 2.6 as compared with Mascot. Moreover, even following a decade of Mascot developments for analyzing CID spectra of tryptic peptides, MS-GFDB (that is not particularly tailored for CID spectra or tryptic peptides) resulted in 28% increase over Mascot in the number of peptide identifications.

Param-Medic

Assesses experimental m/z error and derives parameters to search a Liquid Chromatography-Mass Spectrometry (LC−MS)/MS experiment. Param-Medic assumes that LC−MS/MS experiments are likely to make multiple observations of many peptide ions. It exploits repeated measurements to provide valuable information about the m/z tolerance characteristics of the experiment. The tool was tested on eight data sets from public repositories from a variety of organisms and instruments. The running time is much shorter than that of Preview.

TopPIC / TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization

A software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search. TopPIC efficiently identifies proteoforms with unexpected mutations and post-translational modifications and accurately estimates statistical significance of identifications. It uses several techniques, such indexes, spectral alignment, and a generation function method, to increase its speed, sensitivity, and accuracy.

Cascaded search

An iterative procedure for incorporating information about peptide groups into the database search and confidence estimation procedure. cascade search provides a principled and flexible way to assign peptides to observed spectra with high statistical power, as long as the user is willing to provide in advance a statistical confidence threshold and a series of appropriately ordered peptide databases. Cascade search is particularly valuable in studies that include increasingly diverse types of PTMs and particularly in the context of large proteogenomics studies where unexpected sequence variants must be considered.

ProbIDtree

Identifies automatically multiple precursors from single tandem mass spectrometry (MS/MS) acquisitions in high-throughput proteomics experiments. ProbIDtree is an algorithm that it (i) can identify peptides from collision-induced dissociation (CID) spectra that contain fragment ions from a single precursor ion and compute accurate probabilities, (ii) is able to identify and statistically validate multiple peptide assignments to a single CID spectrum in cases where multiple precursors were concurrently fragmented, (iii) can capture peptide identifications that are missed by conventional database search engine, (iv) takes advantage of the Bayesian ProbID scoring function to identify correct peptides in complex spectra, and (v) can identify a higher number of peptides than conventional search engines.

pTop

A software tool to significantly improve the accuracy and efficiency of mass spectral data analysis in top-down proteomics (TDP). The precursor mass offers crucial clues to infer the potential post-translational modifications co-occurring on the protein, the reliability of which relies heavily on its mass accuracy. Concentrating on detecting the precursors more accurately, a machine-learning model incorporating a variety of spectral features was trained online in pTop via a support vector machine (SVM). pTop employs the sequence tags extracted from the MS/MS spectra and a dynamic programming algorithm to accelerate the search speed, especially for those spectra with multiple post-translational modifications.

GlyDB

Finds reliably glycopeptides from a few thousand collected tandem mass spectrometry (MS/MS) spectra. The GlyDB approach was developed for annotation of low resolution spectra generated by ion trap mass spectra. In the case of simple structures, such as bi-antennary glycans, GlyDB can provide direct assignment. And in the case of more complex glycan structures, it typically selects several potential candidate structures, but in order to assign the most likely structure, additional experiments may be required.

SPLASH / SPectraL hASH

Finds all the spectra that correspond to a specific compound across different databases. SPLASH is a database-independent spectrum identifier that contains separate blocks for defining different layers of information, separated by dashes. The software was developed and refined on a dataset of more than 563000 mass spectra from MassBank, GNPS, HMDB, ReSpect, FiehnLib and NIST. It can be used for cross-reference identification and also allows for coarse similarity comparisons.

CIDentify / Collision-Induced Dissociation identify

Helps to identify unknown peptides by mass spectrometry (MS). CIDentify is a homology-based database search algorithm constructed from the source code for a FASTA homology-based database search program. A loop was inserted to allow the comparison of multiple query sequences to each database sequence and to sum their scores into the score for that database sequence. The lists of candidate sequences produced by the software Lutefisk97 is used as input.

DRIP / Dynamic bayesian network for Rapid Identification of Peptides

A tool which utilizes a dynamic Bayesian network (DBN) for rapid identification of peptides in tandem mass spectra. Given an observed spectrum, DRIP scores a peptide by aligning the peptide's theoretical spectrum and the observed spectrum, i.e., computing the most probable sequence of insertions (spurious observed peaks) and deletions (missing theoretical peaks). DBN inference is efficiently performed utilizing the Graphical Models Toolkit, which allows easy alteration of the model.

PIPI / PTM-Invariant Peptide Identification

A method to achieve PTM-invariant peptide identification. PIPI first codes peptide sequences into Boolean vectors and converts experimental spectra into real-valued vectors. Then, it finds the top 10 peptide-coded vectors for each spectrum-coded vector. After that, PIPI uses a dynamic programming algorithm to localize and characterize modified amino acids. Simulations and real data experiments have shown that PIPI outperforms existing tools by identifying more peptide-spectrum matches (PSMs) and reporting fewer false positives. It also runs much faster than existing tools when the database is large.

FDRAnalysis

Analyses the results from a number of different mass spectrometry (MS)/MS search engines, based on decoy database searching. It accepts results in a number of different formats and outputs a list of candidate peptide and protein identifications in mzIdentML, tab-separated, and comma separated formats. The program acts as a native-to-mzIdentML converter and can combine the results from different search engines to give a set of consensus results that have greater reliability and sensitivity than the results from any single search engine.

Epsilon-Q

Performs automatically multiple spectral library searching, class-specific false-discovery rate (FDR) control and result integration. Epsilon-Q demonstrates good performance in identifying and quantifying proteins by supporting standard mass spectrometry data formats and spectrum-to-spectrum matching. It can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification. The tool allows the user to perform multiple spectral library searching.

IPeak

A peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard.

MsPI / Mass spectrometry Protein Identification

Provides a complete procedure for protein identification by Peptide Mass Fingerprinting (PMF). MsPI is implemented as an exhaustive procedure that: (i) creates a reference database in which the unknown protein is searched, (ii) performs that search, (iii) computes a similarity score for each protein hit retrieved, (iv) creates a random database for a statistical validation of the results. It also includes the removal of contaminant masses and the statistical validation of the results.

MSFragger

Represents a database search tool. MSFragger uses several large proteomic data sets. It empowers the open database search concept for comprehensive identification of peptides and all their modified forms, uncovering dramatic differences in modification rates across experimental samples and conditions. This tool makes open searches feasible even for data sets containing millions of mass spectrometry (MS)/MS spectra. It can performing open searches with variable modifications, making it applicable to data from labeling-based quantitative proteomics experiments.