Manages proteomic mass spectrometry workflows and data analysis. Multiplierz provides a toolset of multiple methods for peptide identification, quantitation, reporting, as well as tools for easily manipulating standard data formats. This software is a Python library compatible with new reporting formats and high-level tools to achieve post-perform proteomic analyses. The architecture of the software environment has seamless integration with native data files via mzAPI.
Facilitates visualization, statistical analysis, and high-quality image and data export. MALDIViz is a comprehensive informatics application for MALDI HTS data. This package provides a theme on top of Shiny, allowing the creation of visually attractive dashboards. It also offers user selectable options for generating a 3D PCA plot, for classification and identification of major sources of variation in the data.
Provides intuitive, yet powerful, instrument control, data acquisition, qualitative and quantitative data analysis, and reporting for Agilent time-of-flight (TOF), quadrupole time-of-flight (Q-TOF), ICP-MS, and triple quadrupole systems. Designed from the ground up to make MS analyses easier from tuning to final report MassHunter Workstation software can be complemented by application-specific MassHunter software packages that provide even more power and stream-lined operation for specialized analytical tasks such as expression profiling.
Offers a platform giving access to Clinical Proteomics Tumor Analysis Consortium (CPTAC) datasets. P-MartCancer is a web application that evaluates peptides to identify the most abundant or reproducible ones and gives a median signal. The program allows users to perform four main functions: (i) quality control processing; (ii) gene or protein quantiﬁcation; (iii) statistics; and (iv) exploratory data analysis.
Allows to analyse shotgun proteomics data. CPFP is a data analysis pipeline that aims to provide a simple interface for core facility staff and clients, and to fully automate the analysis of tandem mass spectrometry (MS/MS) data with multiple search engines. The software consists of a web application, relational database and collection of pipeline scripts. It can be installed locally or started in the Amazon Web Services (AWS) cloud.
Analyzes metabolomics data generated from the 2D gas chromatography time-of-flight mass spectrometry (GCxGC-TOF MS) instrument. MetPP is able to recognize the concentration difference of the spiked-in metabolite standards between sample groups. It is composed of different modules for: retention index matching, peak filtering and merging, peak list alignment, quant mass conversion, normalization, statistical significance tests and pattern recognition.
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.
Provides an interface for basic analysis of mass spectrometry data. mzDesktop gives access to the proteomic analysis algorithms from the library of the Multiplierz software. This software offers several functions existing in Multiplierz but through a graphical user interface. Users can visualize the degree of protein sequence coverage supported by given set of peptide-spectrum match (PSM). It is compatible with mzReports and mzIdentML files.
Manages and combines both identifications and semiquantitative data related to multiple liquid chromatography-mass spectrometry (LC−MS)/MS analyses. hEIDI can be used to compile analyses and retrieve lists of nonredundant protein groups. It allows direct comparison of series of analyses, on the basis of protein groups, while ensuring consistent protein inference and also computing spectral counts. The tool was able to compare pools of analyses in projects for which up to 1500 search results had been combined.
Identifies monoisotopic masses of precursors for tandem mass spectrometry (MS/MS) spectra. pParse proposes a method for determining candidate clusters and classifying them according the sum of the intensity, the similarity of the experimental and the theoretical isotopic distribution, and the similarity of elution profiles. The application was developed to be utilized with Thermo FT/Orbitrap RAW files.
A Java-based proteomics cloud computing pipeline system for peptide and protein identifications. The ProteoCloud pipeline consists of three types of units: (i) a single client-side controller unit, that constitutes the master control for the pipeline; (ii) any number of worker units that will perform the actual identifications; and (iii) a single database unit running the MySQL database instance where all results will be stored.
Enables high-throughput processing of high performance liquid chromatography (HPLC) data. HappyTools is a modular toolkit that can perform all the steps of a completely automated data analysis workflow, including automated peak detection, retention time calibration and peak quantitation. It includes a basic automated peak detection functionality, which identifies the retention time of all signals above a user-defined threshold.
A software tool for the analysis of MALDI data. This is an application that covers the whole process of MALDI data analysis, from data preprocessing to complex data analyses. Mass-Up incorporates the most common analyses, aside from protein identification and focusing in biomarker discovery, such as statistical tests-based biomarker discovery, clustering, PCA, and classification. In addition, other less common analyses such as quality control and biclustering are also included. Therefore, Mass-Up provides users with a wide range of tools to analyze and explore their MALDI data.
Aligns multiple liquid chromatography-mass spectrometry (LC-MS) datasets to one another by clustering mass and chromatographic elution features across datasets. The MultiAlign application provides advanced visualization and manipulation capabilities for LC-MS datasets acquired on high resolution mass spectrometers. Functionalities include overlaid 2D plots, alignment plots, normalizations, and basic statistical comparisons. MultiAlign uses the LCMSWARP algorithm to align LC-MS datasets to a master list (mass tag database or a single LC-MS dataset) and then consolidate features into a consensus map. These features can be matched to an accurate mass and time (AMT) tag database to identify the LC-MS features.
Calculates proteome-wide distances directly from MS/MS data. DISMS2 allows for the choice of the spectrum distance measure and includes different spectra preprocessing and filtering steps that can be tailored to specific situations by parameter optimization. It can be applied to samples from species without database annotation, as on the fresh water snail Radix species and on the foraminifera Amphistegina lessonii and gibbosa.
Enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms, including Mascot, Sequest, and Paragon, as well as cross-comparison of their identification results. The software supports both qualitative and quantitative phosphoproteomics studies, as well as multiple between-group comparisons.