PTM-Shepherd v2.0.5 – A tool for Summarizing Open Search Results

PTM-Shepherd v2.0.5

:: DESCRIPTION

PTM-Shepherd automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PTM-Shepherd

:: MORE INFORMATION

Citation

Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI.
PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.
Mol Cell Proteomics. 2020 Dec 11;20:100018. doi: 10.1074/mcp.TIR120.002216. Epub ahead of print. PMID: 33568339; PMCID: PMC7950090.

TMT-Integrator 4.0.2 – Extract and Combine Channel Abundances from multiple TMT samples

TMT-Integrator 4.0.2

:: DESCRIPTION

TMT-Integrator is a tool that integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Java

:: DOWNLOAD

TMT-Integrator 

:: MORE INFORMATION

Philosopher 5.1.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 5.1.0

:: DESCRIPTION

Philosopher provides easy access to third-party tools and custom algorithms for proteomics analysis, from database searching to functional protein reports. Philosopher is also well-equipped for open search analysis, providing extended versions of PeptideProphet and ProteinProphet for peptide validation and protein inference.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Philosopher

:: MORE INFORMATION

Citation

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI.
Philosopher: a versatile toolkit for shotgun proteomics data analysis.
Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.

MSFragger / FragPipe 22.0 – Peptide Identification in Mass Spectrometry-based Proteomics

MSFragger / FragPipe 22.0

:: DESCRIPTION

MSFragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger – an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

MSFragger / FragPipe

:: MORE INFORMATION

Citation:

Andy Kong, Felipe Leprevost, Dmitry Avtonomov, Dattatreya Mellacheruvu, Alexey Nesvizhskii.
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Nat Meth, May 2017. DOI: 10.1038/nmeth.4256

CRAPome 2.0 – Contaminant Repository for Affinity Purification – Mass Spectrometry data

CRAPome 2.0

:: DESCRIPTION

CRAPome is a database of annotated negative controls contributed by the proteomics research community. It addresses the common problem of distinguishing real interactions from the non-specific background (also known as ‘contaminants’). The database and associated computational tools to score protein interactions are available online.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nat Methods. 2013 Aug;10(8):730-6. doi: 10.1038/nmeth.2557. Epub 2013 Jul 7.
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.
Mellacheruvu D et al.

LinRegPCR 20210614 – Analysis of Quantitative PCR Data

LinRegPCR 20210614

:: DESCRIPTION

LinRegPCR is a program for the analysis of quantitative RT-PCR (qPCR) data resulting from monitoring the PCR reaction with SYBR green or similar fluorescent dyes. The program determines a baseline fluorescence and does a baseline subtraction. Then a Window-of-Linearity is set and PCR efficiencies per sample are calculated. With the mean PCR efficiency per amplicon, the Ct value per sample and the fluorescence threshold set to determnine the Ct, the starting concentration per sample, expressed in arbitrary fluorescence units, is calculated

::DEVELOPER

J. M. Ruijter, S. van der Velden,A. Ilgun @ Heart Failure Research Center (HFRC)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Excel

:: DOWNLOAD

 LinRegPCR

:: MORE INFORMATION

Citation

Ramakers C, Ruijter JM, Deprez RH, Moorman AF. (2003)
Assumption-free analysis of quantitative real-time PCR data
Neurosci Lett 2003 Mar 13;339(1): 62-66

TOPO2 – Create Transmembrane Proteins Images

TOPO2

:: DESCRIPTION

TOPO2 is an open source program written in Python for the creation of transmembrane protein 2D topology images. It makes no attempt to predict the TMDs that it displays. The user needs to supply that information. Residues of interest can be highlighted, if desired.

TOPO2 Web Version

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • Python

:: DOWNLOAD

TOPO2

:: MORE INFORMATION

Contact Susan Jean Johns (email: johns@cgl.ucsf.edu) for more information about the software or if you are having problems with the site.

LDhat 2.2a – Analysis of Recombination Rates from Population Genetic Data

LDhat 2.2a

:: DESCRIPTION

LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.

::DEVELOPER

McVean Group , the Auton lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 LDhat

:: MORE INFORMATION

Citation

Auton and McVean,
Recombination rate estimation in the presence of hotspots.
Genome Research 17(8):1219-27, 2007.

FigTree 1.4.4 – Produce Figures of Phylogenetic Trees

FigTree 1.4.4

:: DESCRIPTION

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. In particular it is designed to display summarized and annotated trees produced by BEAST.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

FigTree

:: MORE INFORMATION

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PerlPrimer 1.1.21 – Open-source PCR Primer Design

PerlPrimer 1.1.21

:: DESCRIPTION

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.

::DEVELOPER

Owen Marshall at Murdoch Childrens Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PerlPrimer

:: MORE INFORMATION

Citation

Owen J. Marshall
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Bioinformatics (2004) 20 (15): 2471-2472.