Skyline 21.1 – Targeted Proteomics Environment

Skyline 21.1

:: DESCRIPTION

Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM – Targeted MS/MS and DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies.

::DEVELOPER

MacCoss Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Skyline

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 9. [Epub ahead of print]
A framework for installable external tools in Skyline.
Broudy D1, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, Maccoss MJ, Maclean B.

DIAlignR v1.1.2 – Chromatogram Alignment for Targeted Proteomics

DIAlignR v1.1.2

:: DESCRIPTION

DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.

::DEVELOPER

Röst Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX
R

:: DOWNLOAD

DIAlignR

:: MORE INFORMATION

Citation

Gupta S, Ahadi S, Zhou W, Röst H.
DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.
Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: 10.1074/mcp.TIR118.001132. Epub 2019 Jan 31. PMID: 30705124; PMCID: PMC6442363.

TAPIR 1.2 – Visualization of Targeted Proteomics data

TAPIR 1.2

:: DESCRIPTION

TAPIR is a visualization software for chromatographic data obtained by mass spectrometry. It provides efficient visualization of high-throughput targeted proteomics experiments.

::DEVELOPER

Röst Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX
Python

:: DOWNLOAD

TAPIR

:: MORE INFORMATION

Citation

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.
Röst H, Rosenberger G, Aebersold R, Malmström L.
Bioinformatics. 2015 Mar 18. pii: btv152.

TRIC – Alignment Tool for Targeted Proteomics

TRIC

:: DESCRIPTION

TRIC is an alignment software for targeted proteomics (SRM or SWATH-MS) data. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate information from all available runs. The input consists of a set of csv files derived from a targeted proteomics experiment generated by OpenSWATH (using either mProphet or pyProphet) or generated by Peakview.

::DEVELOPER

Aebersold Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TRIC

:: MORE INFORMATION

Citation

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.
Röst HL, Liu Y, D’Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R.
Nat Methods. 2016 Aug 1. doi: 10.1038/nmeth.3954.

MyMRM 1.2 – Designing Targeted Proteomics Methods

MyMRM 1.2

:: DESCRIPTION

MyMRM is a simple software tool to aid proteomic laboratories designing targeted proteomics methods for their own equipment by using the data of their shotgun experiments.

::DEVELOPER

EhuBio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Web Server

:: DOWNLOAD

MyMRM

:: MORE INFORMATION