Search Results for "proteomics"
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Showing 83 open source projects for "proteomics"
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Pro-statTarget is Portable Version and standalone software, provides a graphical user interface for quality control based signal drift correction (QC-RFSC), integration of data from multi-batch MS-based experiments, and the comprehensive statistical analysis in metabolomics and proteomics. Author: Hemi Luan Maintainer: Hemi Luan Citation (from within R, enter citation("statTarget")): Luan H, Ji F, Chen Y, Cai Z (2018). “statTarget: a streamlined tool for signal drift correction and interpretations of quantitative mass spectrometry-based omics data.” Analytica Chimica Acta, 1036, 66-72.
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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Seqs Extractor is a useful tool, and can reduce ambiguities in analyses which uses BLAST command ine, commonly in the next generation sequencing, Transcriptomics, Proteomics, etc and help extract BLASTed sequences and sequences that contains microsatellites. Seqs Extrator also turns the BLAST command line more friendly.
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Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled MS data are based on sequence database searching. We present a novel quantitation pipeline which integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter (FPF) using various spectral features for filtering. The combined database and spectral library searching results in...
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MANTI
MANTI - Mastering Advanced N-Termini Interpretation
...The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred from different other source files from the corresponding folder. Maybe also useful for normal proteomics purposes but this script is heavily optimized for protein neo-termini identification and validation. A graphical interface is available as Yoğurtlu_MANTI (a Perl/Tk script) + execut. application versions for Win1x without the need to have Perl installed locally. For a very detailed explanation of script parameters and the evaluation strategy, please consult the extensive manual PDF -
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dataMAPPs
R based pipeline for MHC-associated peptide proteomics (MAPPs) data
dataMAPPs allows routine and efficient processing of data from immunogenicity studies applying the MAPPs peptidomics technology to detect potential MHCI- or MHC-II epitopes as presented by dendritic cells (DC). It features quality control of the raw data, across-sample/across-donor normalization and visualization of results in a heatmap style (heatMAPPs). dataMAPPs' core is a generic R library that can be tailored to specific projects via dedicated control scripts which also allow... -
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MScDB
A Mass Spectrometry Centric Protein Sequence Database for Proteomics
Protein sequence databases are indispensable tools for life science research including mass spectrometry (MS)-based proteomics. In current database construction processes, sequence similarity clustering is used to reduce redundancies in the source data. Albeit powerful, it ignores the peptide centric nature of proteomic data and the fact that MS is able to distinguish similar sequences. Therefore, we introduce an approach that structures the protein sequence space at the peptide level using theoretical and empirical information from large-scale proteomic data to generate a mass spectrometry centric protein sequence database (MScDB). ... -
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KidneyExplorer
Kidney proteomics data explorer enables you to investigate diseases
KidneyExplorer enables you to interactively survey kidney proteomics datasets from different kidney disease models. Here you can download the corresponding SQL database dumps. The original website for the shiny app is: https://kidneyapp.shinyapps.io/kidneyorganoids/ -
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Calibr is a tool for the spectrum-centric analysis of DIA data against DDA-based spectral library, to perform optimization of spectrum preprocessing and calculating various spectral similarity measures as features for validation. In addition to spectral similarity measures, Calibr provides other two types of features related to precursor ion and spectrum property and statistics from spectrum-spectrum matches (SSMs) for machine-learning based validation. To support users to conveniently...
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PINCIS
PINCIS.pl is a Perl bioinf. script to analyze PICS data
...Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create). -
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ModST
A tool to search post-translational modifications in a blind mode
ModST (pronounced as modest) is a tool to search post-translational modifications (PTMs) in mass spectrometry data in an unrestrictive manner. It can search for hundreds of modification without any user provided information for variable modifications. Due to data level parallelization implemented through perl it is fast, portable and easy to use to identify and analyse PTMs in MS/MS data. -
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Calis-p
Estimates delta13C of species in a microbiome from proteome data
Calis-p (The CALgary approach to ISotopes in proteomics) is a java application to estimate isotopic composition (e.g. delta13C or delta15N) of individual species in a microbial community from a proteomic dataset. Calis-p 2.0 handles both natural isotope abundances and data from labelling experiments such as stable isotope probing (SIP). It requires a mzIdent (or target spectrum match) and mzML files as the input and requires about 1 min per mzML file with 10 threads and needs <10 Gb of RAM. ... -
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Proteomics Documents
Open-Access Documents delivered to be used by the Proteomics community
Open-Access Documents delivered to be used by the Proteomics community: - MIAPE-SP v1: download it at https://sourceforge.net/projects/proteomicsdocs.lp-csic-uab.p/files/MIAPE_SP_v1.pdf/download -
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MANTI.pl / muda.pl
muda.pl - MQ unified data assembler
...The central anchor for the data congregation is the modificationSpecificPeptides.txt file - additional data is inferred from different other source files from the MaxQuant txt folder but the starting point for the data assembly is solely the modificationSpecificPeptides.txt file. Maybe also useful for normal proteomics purposes but this script is heavily optimized for protein neo-termini identification and validation. For a more thorough explanation of script parameters and evaluation strategy, please consult the extensive manual PDF. -
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QuantWiz-IQ is a tool for reporter based MS/MS quantitation using iTRAQ or TMT tags from shotgun proteomics experiments. It supports MGF and HUPO-PSI mzML format as input. It supports quantitation of reporter tags with iTRAQ 4-plex or 8-plex. It also supports TMT 2/6/10-plex quantitation.
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DIAFree
a workflow use to identify and quantify protein from DIA
# DIAFree DIAFree is a workflow use to identify and quantify protein from spectra(.raw/.mzML). Please alter basic.ini to reset the environments and then click on DIAFreeGUI.exe, then you are free to use! spectra lib & predicted spectra lib(use pDeep) are unable to use only because I do not finish the UI logic yet. This is a simple introduction because network issues make Upload To Github unable to finish! Please download it from: -
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Python4Proteomics Course
Python course for Proteomics analysis
Python course (in Spanish) for Proteomics analysis using basically Jupyter NoteBooks. For more information, you can have a look at the readme.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/p4p/code/ci/default/tree/readme.md -
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LymPHOS2
LymPHOS2 Web-App
...Proteome Res. 2008, 7, 5167-5176. DOI: 10.1021/pr800500r - Ovelleiro, D., Carrascal, M., Casas, V., Abian, J., LymPHOS: design of a phosphosite database of primary human T cells. Proteomics 2009, 9, 3741–3751. DOI: 10.1002/pmic.200800701 - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., Abian, J., A collection of open source applications for mass spectrometry data mining. Proteomics 2014, 20, 2275-2279. DOI: 10.1002/pmic.20140012 -
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FastaTools
Performs several operations to Fasta protein databases
...For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/fastatools/code/ci/default/tree/README.md Or you can download the Documentation an Tutorial PDF file in the Files section: https://sourceforge.net/projects/fastatools.lp-csic-uab.p/files/FastaTools%20Documentation%20and%20Tutorials.pdf - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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luciphor2
A generalized PTM localization tool for proteomics.
This is a generalized version of phospho-site localization tool called luciphor http://luciphor.sourceforge.net/ This version of the program offers three improvements: 1) It will run on any operating system that can use JAVA. 2) It can score any PTM 3) It can accept input from any search tool. -
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Mass-Up
MALDI-TOF data analysis tool
Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data. -
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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Lirex
A Package for Identification of Long Inverted Repeats in Genomes
...Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. For more details, please refer to Genomics, Proteomics and Bioinformatics 2017, 15:141-146 by Y. Wang and J.M. Huang. -
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Central Proteomics Facilities Pipeline
A data analysis pipeline for shotgun mass-spectrometry proteomics.
CPFP provides a pipeline for the analysis of MS/MS proteomic data, targeted at the needs of central proteomics facilities. == Project Status - Updated January 3rd 2019 == CPFP has not been actively developed since 2014, when I left the proteomics group at UTSW. To access up-to-date algorithms for the analysis of proteomics data, other tools would now be preferred. However: * Limited fixes have been made on the main master branch by Phil Charles at the University of Oxford...
