Available tools

Web Application

CurtainSharing your total proteomics data with only a click
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For visualization of differential analysis of total proteomics data. Curtain enable easy sharing of differential analysis with no installation of additional software but your web browser.

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Curtain PTMSharing your PTM proteomics data with only a click
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For visualization of differential analysis of PTM proteomics data. Similar to Curtain, however, with PTM, the tool also aggregate extra data from other PTM databases for comparison between yours and the current knowledge base.

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CopicaA static database of protein copy numbers from deep profiling proteomics data
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Copica contains a collections of copy number derived from mass spectrometry analysis of deep profiling proteomics obtained using proteomics ruler extension from Perseus proteomics data analysis suite.

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CupcakeAn open source e-lab notebook, samples, metadata and proteomics job management web application

Cupcake was originally developed as a e-lab notebook that includes various advanced function like timers, voice and video recorder, sample tracker and many more. Recently, it has been extended to management of proteomics job submission and metadata, specifically in SDRF format. It combined the typical proteomics MS job submission for MS experiment to a facility with an SDRF metadata builder ensuring that any job submitted to the facility would also have a compliant SDRF file.

Go to demoGitHub BackendGitHub Frontend
Cinder A web application for indexing, collating and searching of proteomics downstream analysis results

Cinder is a web application that allow users to upload their proteomics analysis results and index them for searching. The application can be used in conjunction with other proteomics analysis tools like Curtain and CurtainPTM where it would automatically import data from submitted Curtain or CurtainPTM links as well as the volcano plot and all its settings.

Go to demoGitHub BackendGitHub Frontend

Python Packages and Modules

sequalA Python package for all your amino acid sequence parsing need
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Sequal can be used for reading and formatting protein sequences with and without modifications whether or not they are placed as suffix or prefix to the amino acid residue. With it there is also a minimal support for certain Mass Spectrometry related task within the package.

PypiGitHub
UniProt Web ParserA Python package for querying sequence data from the UniProt biosequence database through its REST API
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The package is simple and can either choose to query data as fasta or in tabulated text form with or without all isoforms. For a synchronous workflow, the tool use Python requests module while aiohttp is used in case of asynchronous integration.

PypiGitHub
DiannPyA Python package for producing additional reports from Diann analysis
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The package use information provided by Diann in couple with sample condition label to produce additional plots and produce mapping of each ptm from peptides to those of the original sequence.

PypiGitHub
Proteomic RulerA Python package for calculating copy number of protein content in deep profiling proteomics experiment from mass spectrometry data
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The package is a direct adaptation of the same algorithm used by a plugin of the same name in Perseus proteomics analysis suite for calculation of copy number based on amount of histone within the sample.

PypiGitHub
codxA Python package for building fasta library of variation of exon combination of protein
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The package use gene ids or uniprot accession ids as input to retrieve refseqgene record from NCBI and then use the exon information to build a fasta library of all possible combination of exons with or without introns.

PypiGitHub

Node.JS Modules

uniprotparserjsA JS/TS package for retrieving data from the UniProt Rest API
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Similar to my uniprotparser python package, uniprotparserjs can be used to get UniProt data in tabulated text format from the using the REST API. The package can be used both in Node and Web browser environments.

npmGitHub
SequalJSA JS/TS package for parsing and writing ProForma peptide sequences

Similar to my sequal python package, SequalJS can be used on any web-based and node.js resources for reading and writing ProForma compliant protein sequences.

npmGitHubPreview & Doc