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Skyline

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A freely-available and open source Windows client application for building selected reaction monitoring (SRM)/multiple reaction monitoring (MRM), parallel reaction monitoring (PRM - targeted MS/MS), data independent acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. Skyline aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies.

OpenMS

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Allows to manage and analyse Liquid chromatography coupled to mass spectrometry (LC-MS) data. OpenMS is a programming library and tool collection integrated into full-featured workflow systems, such as KNIME, Galaxy and WS-PGRADE, to facilitate bioinformatics research in the field of MS on all levels. The software provides pre-built and ready-to-use tools for analysis of both proteomics and non-targeted metabolomics data.

GNPS / Global Natural Products Social Molecular Networking

An open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS provides a community-led knowledge space in which NP data can be shared, analyzed, and annotated by researchers worldwide. It enables a cycle of annotation in which users curate data, continuous dereplication enables product identification, and a knowledge base of reference spectral libraries and public data sets is created.

SWATH2stats

A package intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation. SWATH2stats allows to i) annotate the data, ii) analyze reproducibility across replicates, iii) estimate the FDR, iv) filter for assays meeting certain confidence or other criteria and v) convert the large proteomic datasets to the respective input formats of the downstream analysis tools MSstats, mapDIA, and aLFQ.

MAPDIA

A software package for statistical analysis of differential protein expression using DIA fragment-level intensities. The workflow consists of three major steps: intensity normalization, peptide/fragment selection, and statistical analysis. First, mapDIA offers normalization of fragment-level intensities by total intensity sums as well as a novel alternative normalization by local intensity sums in retention time space. Second, mapDIA removes outlier observations and selects peptides/fragments that preserve the major quantitative patterns across all samples for each protein. Last, using the selected fragments and peptides, mapDIA performs model-based statistical significance analysis of protein-level differential expression between specified groups of samples.

MSstats

An R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.

LFQuant / label-free fast quantitative

Analyses high-resolution LC-MS/MS proteomics data based on database searching. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant performs better than MaxQuant and IDEAL-Q, two common quantification software packages, in terms of both precision and accuracy, and consumes significantly less processing time.

MRMer

Obsolete
Allows to manage highly complex multiple reaction monitoring mass spectrometry (MRM-MS) experiments. MRMer functions in an instrument-agnostic fashion using an updated standard of the mzXML format. The software automatically extracts and groups precursor-product pairs for visual validation of co-elution and calculates absolute and relative area under the curves (AUCs) for standard and absolute quantification/stable isotope labeling by amino acids in cell culture (AQUA/SILAC) type experiments, respectively. It also permits the quantitative analysis experiments including heavy and light isotopic peptide pairs.