Skyline Tool Store 
BiodiversityPlugin
BiodiversityPlugin

Version 1.0.5

Computational Proteomics Group, Pacific Northwest National Laboratory

http://omics.pnl.gov/project-data/biodiversity-library

The PNNL Biodiversity Library is designed to provide an easy interface for retrieving mass spectrometry data and importing it to Skyline, exposing peptides identified in MS/MS by allowing users to select an organism and biological pathway of interest. The Biodiversity Library catalogs MS/MS spectra from over 3 million peptides and 230,000 proteins from 118 distinct organisms across the tree of life all cross referenced to KEGG pathways for intuitive biological interpretation. The Library was developed by Sam Payne at Pacific Northwest National Laboratory with data collected over 10+ years in hundreds of collaborative projects. This application requires Skyline Version 3.1.1.7490 or later.
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Cross-link Transition Calculator
Cross-link Transition Calculator

Version 1.2

Bruce Lab, University of Washington

http://brucelab.gs.washington.edu/software.html

This tool calculates fragment ion transitions for cross-linked peptide pairs. These can be used for PRM and SRM experiments. The program calculates the m/z values for the theoretical fragment ions including the full length released peptides, long arm ions resulting from the cleavage of a single PIR labile bond, and the b-type and y-type ions from both cross-linked peptides assuming both PIR labile bonds were cleaved. For non-cleavable cross-linkers, intact precursor m/z ions and b-type and y-type fragment ions are reported.
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MPPReport
MPPReport

Version 1.0

Agilent Technologies

http://www.agilent.com/

The MPPReport tool allows you to export results for analysis in Agilent's Mass Profiler Professional multivariate statistics software. Using a combination of advanced processing capabilities and powerful statistical and mathematical models to analyze complex proteomics data sets, Mass Profiler Professional lets you easily classify, compare, and analyze sample groups. Pathway Architect, an optional software module for Mass Profiler Professional, allows users to take the results from single or multi-omics experiments and map them onto canonical biological pathways, concurrently analyzing, visualizing, and interpreting pathway information. This pathway-centric workflow speeds the route from discovery and insight to validation. It also enables researchers to efficiently plan and execute their next series of experiments.
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MS1Probe
MS1Probe

Version 1.1

Gibson Lab, The Buck Institute for Research on Aging

MS1Probe can further process MS1 full scan data originally analyzed in Skyline, and is designed to be capable of high throughput statistical quantification of Skyline MS1 Filtering datasets. MS1Probe creates a tabular statistical report that includes the average peak area, standard deviation, coefficient of variation, fold changes over two custom conditions, and a q value for the corresponding fold changes.

DIAprobe is unique in that it calculates the sum of fragment ions from independent acquisition data, originally analyzed in Skyline, and is designed for high throughput statistical quantitation of Skyline SWATH datasets. New features to the statistical tool, DIAprobe, include calculating peak area averages, variability measures, fold change between different sample conditions, corresponding q-values, and custom graphics generated in R. These tabular and graphical statistical analyses are all created with the click of a button.
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MSstats
MSstats

Version 3.8.3

Vitek Lab, Purdue University

http://www.msstats.org/

MSstats is an R package for statistical relative quantification of proteins and peptides in global, targeted and data-independent proteomics. It handles shotgun, label-free and label-based (universal synthetic peptide-based) SRM (selected reaction monitoring), and SWATH/DIA (data independent acquisition) experiments. It can be used for experiments with complex designs (e.g. comparing more than two experimental conditions, or a time course).

Input for MSstats requires transition-level identified and quantified peaks information, including protein id, peptide id, transition id, label type (if labeling is used), condition name, biological replicate id, MS run, and intensity (quantified by either peak area or peak apex). The input tables can be exported from other software for mass spectrometer data, such as Skyline. MSstats provides functionalities for three types of analysis: (1) data processing and visualization for quality control, (2) model-based statistical analysis, in particular testing for differential protein abundance between condition and estimation of protein abundance in individual biological samples or conditions on a relative scale, and (3) model-based calculation of a sample size for a future experiment, while using the current dataset as a pilot study for variance estimation. The statistical analysis is based on a family of linear mixed-effects models. The analysis produces tables with numerical outputs, as well as visualization plots. MSstats package, example datasets with R scripts and documentation are available at http://www.msstats.org.
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Population Variation
Population Variation

Version 2.0.0

Computational Proteomics Group, Pacific Northwest National Laboratory

http://omics.pnl.gov/software/PopulationVariation.php

The Population Variation plug-in for Skyline presents the variant data from dbSNP and the 1000 Genome project for mutations with a calculated minor allele frequency. Three kinds of mutations that alter protein coding sequences are reported: non-synonymous variants that change a single amino acid, and frame-shift and stop-gain mutations that alter all downstream amino acids. The plug-in is regularly updated to keep current with dbSNP releases. (build 137)
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Prego
Prego

Version 1.0.1

MacCoss Lab, University of Washington

PREGO Peptide Response Predictor
PREGO is a software tool that predicts high responding peptides for SRM experiments. PREGO predicts peptide responses with
an artificial neural network trained using 11 minimally redundant, maximally relevant properties. Crucial to its success,
PREGO is trained using fragment ion intensities of equimolar synthetic peptides extracted from data independent acquisition
(DIA) experiments.
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Proteotypic Peptide Viewer
Proteotypic Peptide Viewer

Version 1.0.2

Computational Proteomics Group, Pacific Northwest National Laboratory

http://omics.pnl.gov/project-data/

The Proteotypic Peptide Viewer shows observed peptides in homologous proteins. Data backing the viewer comes from PNNL's Biodiversity Library with more than 100 organisms. The wizard helps users view their favorite protein using the following steps.
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Protter
Protter

Version 1.0.1

IMSB (ETH Zurich)

http://wlab.ethz.ch/protter/

Protter visualizes your peptides on the protein sequence in the context of its transmembrane topology and other features as annotated in UniProt, PeptideAtlas, HPA, etc.
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QuaSAR
QuaSAR

Version 1.32

Broad Institute of MIT and Harvard

http://genepattern.broadinstitute.org/gp/pages/index.jsf?lsid=QuaSAR

QuaSAR implements a suite of tools for QC, analysis and visualization of data from quantitative MRM-MS experiments including assay configuration, calibration curves and new sample analysis. For every monitored peptide the module provides statistical measures such as, coefficient of variation (CV), regression slope and intercept (with confidence intervals), interference detection, and limits of detection (LOD) and quantification (LOQ). It also provides succinct visual summaries of various results including reproducibility, interferences and detection limits. Statistics and visualization are integrated to enable effective data interpretation, understanding and insight.
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Skyline Gadget for Garuda
Skyline Gadget for Garuda

Version 1.0

Shimadzu

http://www.garuda-alliance.org/gadgetpack/shimadzu/

Garuda is an open, community-driven platform for systems biology. It supports multitude of ways to process, visualize and interpret the data by providing a framework to connect and navigate through different analytics applications called “gadgets”. This external tool exports the peptide quantitative data analyzed by Skyline in as a CVS file that can be fed into Shimadzu Gadget in Garuda Platform for subsequent analysis, such as statistical analysis, displaying on the metabolic pathway map, combining with the metabolite data and so forth. Enjoy discovering the system of life by multi-omics analysis!
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SProCoP
SProCoP

Version 1.3

Bereman Lab, NCSU

http://www4.ncsu.edu/~msberema/

Statistical process control (SPC) is a robust set of tools that aids in the visualization, detection, and identification of assignable causes of variation in any process that creates products, services, or information. A tool has been developed termed Statistical Process Control in Proteomics (SProCoP) which implements aspects of SPC (e.g., control charts and Pareto analysis) into the Skyline software. It provides real time evaluation of the chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution); and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts and boxplots. Its power as a quality control procedure lies in its emphasis on early detection of the LC MS/MS process performing outside experimentally-defined thresholds. SProCoP is compatible with both low resolution (i.e, SRM) and high resolution targeted MS/MS or MS1 filtering experiments. UPDATE: 1) New PCA analysis and multivariate control charts; 2) Now able to track SIL peptide abundance; 3) Fixed issue with NA values; 4) Reference set colored green and outliers are red.
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TFExport
TFExport

Version 1.0

ThermoFisher

https://www.thermofisher.com/

TFExport is a tool that will export relevant information from peptides in a Skyline document for the purpose of importing directly into a Trace Finder compound database. Once a method has been optimized and finalized, information about each peptide (protein name, precursor m/z and z, product ion m/z and z, retention time, peak areas and ranking of product ions) is exported into a format that Trace Finder can read and use to process .raw files.
 
For best results, requirements include at least one data file with results for all peptides in the Skyline document. Product ions (“Targets”) can be exported individually and processed in parallel in Trace Finder, or one product ion per peptide (the most intense, by default) can be used for quantification and the remainder are used as confirming ions. Internal standards can be defined during the export process and analytes/internal standards can be linked once the file is imported into Trace Finder.
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