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The flowchart below illustrates the computational pipeline used to identify peptides from LC-MS/MS experiments.

Pepitome is a spectral library search engine. MyriMatch is a database search engine. TagRecon is a mutation-tolerant search engine, which reconciles partial sequence tags generated by DirecTag against a protein database. IDPicker is a parsimonious protein assembler, which filters peptide identifications using a target FDR. References associated with all software are available here.

Our software supports a total of 12 different raw data formats. More information about the supported formats can be found here.
Executables and source code for all projects are available free of charge under the terms of the Apache License, Version 2.0.


BumberDash Proteomics analysis for desktop PCs

This friendly application provides a graphical user interface for configuring, queueing, and running analysis tools in the Bumbershoot suite. Currently MyriMatch and DirecTag/TagRecon are supported. These tools can fully utilize the multi-core desktop PCs common today.

Documentation



DirecTag Tagging MS/MS without abstraction

Sequence tagging is designed to complement database search tools like MyriMatch by providing partial explanations for experimental data. The partial explanations (tags) can later be used to reconcile against a protein database, usually allowing for modifications and/or mutations because of the extreme filtration of the search space by the tags. DirecTag has been tested with many instrument types. It can parallelize its task across multiple processors via threading or computer nodes via the Message Passing Interface.

Documentation



TagRecon Sequence tag reconciliation

Sequence tagging is designed to complement database search tools like MyriMatch by providing partial explanations for experimental data. These partial explanations (tags) are reconciled against a protein database while making allowances for unanticipated mutations and/or posttranslational modifications. TagRecon has been tested with data from many instrument types. The software can take advantage of both multi-core CPUs or multi-node computer clusters (via Message Passing Interface).

Documentation



MyriMatch Identifying MS/MS through database search

MyriMatch is a tool designed to take experimental data from shotgun proteomics experiments and compare those spectra against sequences in a known database of proteins. Whether the program is being run in a single-computer environment or across an entire cluster of processing nodes, it is able to optimally divide work in a much more efficient way than many other database search programs. This is because it only generates candidate sequences from the known database once for the entire set of spectra instead of once for every spectrum. Thus, for each candidate sequence generated, it is compared against every spectrum. The spectra keep a certain (user-defined) number of candidate sequences that had the highest scores.

Documentation



Pepitome Probabilistic scoring systems for spectral library searches

Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs.

Documentation



IDPicker 2 Filtering, assembling, and reporting parsimonious protein identifications

Protein assembly is the process of transforming raw peptide identifications into confident protein identifications. IDPicker infers score thresholds to achieve target false discovery rates (FDR) among peptide identifications. The software can remove artifactual proteins for more parsimonious protein reporting. IDPicker's HTML protein reports cluster indiscernible proteins and those that share peptides, making it far easier to learn the biological lessons presented by each sample. It applies a user-specified experimental hierarchy to collections of peptide identifications and enables users to track the number of spectra or peptides observed for a given protein across multiple experiments.

Documentation



IDPicker 3 Filtering, assembling, and reporting parsimonious protein identifications

Protein assembly is the process of transforming raw peptide identifications into confident protein identifications. IDPicker infers score thresholds to achieve target false discovery rates (FDR) among peptide identifications. The software can remove artifactual proteins for more parsimonious protein reporting. IDPicker 3's highly interactive and flexible interface enables sophisticated interrogation of your data, making it far easier to learn the biological lessons presented by each sample. It applies a user-specified experimental hierarchy to collections of peptide identifications and enables users to track the number of spectra or peptides observed for a given protein across multiple experiments.

Documentation



ScanRanker Assessing quality of tandem mass spectra via sequence tagging

Frequently thousands of spectra could be generated in a typical proteomics experiment, but only a small fraction of spectra can be confidently identified. The remaining unassigned spectra consist of both low quality and high quality spectra. ScanRanker is a tool that assess spectral quality via sequence tagging. It can be used not only to filter low quality spectra prior to database search, but also to find unassigned high quality spectra that evade identification through database search. ScanRanker generates a new subset of spectra, enabling the selection of high quality spectra for de novo sequencing, cross-linking or other subsequent analysis. A graphical interface is provided to analyze ScanRanker results, enabling interactive manual validate of peptide-spectrum matches.

Documentation



QuaMeter Quantifying quality metrics for LC-MS/MS runs

Technologies for proteomic identification via LC-MS/MS rely on a complex series of experiments: protein denaturation and digestion, LC separation of peptides followed by electrospray ionization, tandem mass spectrometry, and proteome informatics. Variation in the performance for any of these elements may impact proteomic identification. The 2009 publication of LC-MS/MS quality metrics by Paul Rudnick at NIST, working in collaboration with the NCI CPTAC network, introduced a set of metrics that span this complex process (Rudnick et al., 2010), enabling recognition of components that were operating at variance with their typical performance. NIST developed the MSQC tool to calculate these metrics. QuaMeter provides the capabilities of MSQC without requiring the same complex input file set.

Documentation



SQTer

SQTer is no longer maintained. Use the Out2XML converter from the Trans Proteomic Pipeline instead.



PSIco+LibMSR

PSIco and LibMSR are obsolete. All of their functionality (and more) is available in msconvert and ProteoWizard.



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