An R/Bioconductor package for the analysis of quantitative proteomics experiments that use isobaric tagging. MSnbase provides an exploratory data analysis framework for reproducible research, allowing raw data import, quality control, visualization, data processing and quantitation. MSnbase allows direct integration of quantitative proteomics data with additional facilities for statistical analysis provided by the Bioconductor project.
A method to correlate tandem mass spectra of sample RNA nucleolytic fragments with an RNA nucleotide sequence in a DNA/RNA sequence database, thereby allowing tandem mass spectrometry (MS/MS)-based identification of RNA in biological samples. Ariadne, a unique web-based database search engine, identifies RNA by two probability-based evaluation steps of MS/MS data.
A versatile set of functions to generate assay panels from spectral libraries for use in targeted data extraction methods (SWATH/DIA) in the area of proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.
A fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses.
Assesses linear copolymers composition matrices from mass spectrometry (MS) spectra data. COCONUT is an open source software able to perform spectral preprocessing including centroiding and baseline correction as well as to compute isotope patterns, evaluate copolymer composition or solve isobaric species. The software had been tested on simulated mass spectra from different monomers.
A data processing tool for targeted high-throughput MALDI-MS data extraction. MassyTools is capable of calibrating spectra, extracting data, and performing quality control calculations based on a user-defined list of glycan or glycopeptide compositions. Typical examples of output include relative areas after background subtraction, isotopic pattern-based quality scores, spectral quality scores, and signal-to-noise ratios.
Normalizes the uploaded data using twelve different well known normalization methods and compares the resulting data based on quantitative and qualitative parameters. Normalyzer is completely automated online tool for data normalization. There are no parameters to configure and no scripts to install.
Computes analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for "Tier 2" assays - that is, non-clinical assays sufficient enough to measure changes due to both biological and experimental perturbations. Computed measures include; limit of detection, lower limit of quantification, linearity, carry-over, partial validation of specificity, and upper limit of quantification. MRMPlus streamlines assay development analytical workflow and therefore minimizes error predisposition.
Facilitates processing of the post-acquisition data files and validation of quantification result for scale selected reaction monitoring (SRM). SRMBuilder analyzes large SRM data from multiple file formats, validate the quantification results either automatically or manually, and export the final quantification results. It provides a user friendly graphic interface for manual check and elution time adjustment at transition/compound/sample level. SRMBuilder is a part of the software suite ProteomicsTools.
Improves the capabilities for open-source software development in proteomics, including re-analysis and visualization of data sets. Importantly, mzQuantML ensures that data sets submitted to public repositories contain a trace of how protein values were calculated via peptide intermediates, back to regions in two-dimensional LC-MS space. This data standard can represent quantitative information about regions in two-dimensional retention time versus mass/charge space (called features), peptides, and proteins and protein groups (where there is ambiguity regarding peptide-to-protein inference), and it offers limited support for small molecule (metabolomic) data.
Allows users to characterize tandem mass spectrometry (MS/MS) spectra for all classes synthetic polymers. PLUMS offers a graphical interface able to detect both the monomer recurring unit of different homopolymers and fragmentation series, and can be used with homopolymers with different cationization agents. Users can choose from a selection of formulae which one is the most fitted and derived its corresponding results.
Provides a method for picking high quality transitions and multiple reactions monitoring (MRM) runs without adding external information. MRM pre-processing is an R package that includes two mains features dedicated to normalization and quality assessment, with the aim of assisting users in downstream analysis or developing MRM assay. The application can be used with both label-free and other quantified data.
Allows users to pre-process label-free multiple reaction monitoring (MRM) data. MSq aims to provide an automatic method for assisting in removing inaccurate transitions, problematic peptides or outlying runs for multiple features such as downstream analysis. The application also includes functionalities for performing data normalization as well as quality assessment.
Identifies and adjusts interference in targeted mass spectrometry data. MADIC features Pandas data structures to detect trace peptide quantities through stringent peptide quality control criteria and interference identification. If the raw data is compatible with Skyline-daily, this software can utilize selected reaction monitoring (SRM) and multiple reaction monitoring (MRM) data.
Offers a method for library identification and confirmation. tMRM is a platform which is able to work with all Agilent Triple Quadrupole liquid chromatography–mass spectrometry (LC/MS) systems. This approach can be used for the confirmation of target analytes and, more generally, for compound identification.
Calculates peptide and glycopeptide masses. Swiss Mass Abacus is purposefully kept as simple as a basic calculator executing arithmetic operations. It applies a calculator using algebraic precedence which means that binary operators are always applied in the order: exponents and roots, then multiplication and division, and finally addition and subtraction.
A set of algorithms and tools intended for analysis of data independent acquisition mass spectrometry (DIA-MS) data, using a targeted extraction strategy. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset.