MSstatsPTM - Statistical Characterization of Post-translational Modifications

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

Last updated 24 days ago

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolpost-translational-modification

7.93 score 8 stars 2 packages 32 scripts 386 downloads

MSstatsTMT - Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Last updated 7 days ago

immunooncologymassspectrometryproteomicssoftware

6.50 score 3 packages 35 scripts 450 downloads

MSstatsShiny - MSstats GUI for Statistical Anaylsis of Proteomics Experiments

MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.

Last updated 24 days ago

immunooncologymassspectrometryproteomicssoftwareshinyappsdifferentialexpressiononechanneltwochannelnormalizationqualitycontrolgui

6.47 score 13 stars 4 scripts 218 downloads

MSstatsLiP - LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

Last updated 24 days ago

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrol

5.60 score 5 stars 5 scripts 188 downloads

MSstatsLOBD - Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) <doi:10.1074/mcp.RA117.000322>.

Last updated 24 days ago

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolmass-spectrometry

4.30 score 1 scripts 140 downloads