Software – Consortium for Top-Down Proteomics (2024)

FLASHIda

Link

FLASHIda is an intelligent online data acquisition algorithm for top-down proteomics that ensures the real-time selection of high-quality precursors of diverse proteoforms. It ensures the real-time selection of high-quality precursors of diverse proteforms, using an instant m/z-intensity to mass-quality spectral transformation coupled with a machine learning-based quality assessment.

MASH Suite

Link

MASH Suite is a versatile software interface for processing high-resolution mass spectrometry data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution mass spectrometry data and manually validate automatically processed results.

MetaMorpheus

Link

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

MS-Align+

Link

MS-Align+ is a software tool for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. MS-Align+ is fast in identifying unexpected post-translational modifications. In addition, MS-Align+ reports statistical significance of top-down protein identifications.

MS-DECONV

Link

MS-Deconv is a software tool for top down spectral deconvolution. MS-Deconv uses a combinatorial algorithm. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph. In contrast with other approaches, the algorithm scores sets of envelopes rather than individual envelopes.

MSPathFinder

Link

Similar to database search engines for bottom-up, it takes a fasta file, a spectrum file, and a list of modifications as an input and reports proteoform spectrum matches (PrSMs) and their scores.

ProSight Lite

Link

ProSight Lite is a free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations.

ProSight PTM

Link

ProSight PTM 2.0 allows identification and characterization of both intact proteins and peptides. ProSight Warehouses are annotated with all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (SNPs) using Shotgun Annotation. ProSightPTM allows the user to search their tandem MS data against proteome warehouses containing the known biological complexity present in UniProt.

Proteoform Characterization Tool

Link

This tool (beta) was developed for scoring proteoforms of multiply-modified proteins. The input is: (i) an intact mass, (ii) a fragment ion dataset, (iii) a protein sequence, and (iv) the specific kinds of PTMs to be considered. The output is given as a [Phrap] score, where the higher scores are better.

ProteoformSuite

Link

Software for constructing, quantifying, and visualizing proteoform families.

Protter

Link

The ability to integrate and visualize experimental proteomic evidence in the context of rich protein feature annotations represents an unmet need of the proteomics community. Protter is a web-based tool that supports interactive protein data analysis and hypothesis generation by visualizing both annotated sequence features and experimental proteomic data in the context of protein topology. Protter supports numerous proteomic file formats and automatically integrates a variety of reference protein annotation sources, which can be readily extended via modular plug-ins.

pTop

Link

pTop is a software dedicated for the analysis of intact protein using mass spectrometry. It can support the complex data sets with ultra-modifications.

Search Engine for Multi-Proteoform Complexes

Link

Here we combine the CORUM and UniProt databases to create candidates for an error-tolerant search engine designed for hierarchical top-down analyses, identification, and scoring of multi-proteoform complexes by native mass spectrometry.

SpectroGene

Link

SpectroGene is a tool for top-down protein identification using unannotated bacterial genome. SpectroGene could be used for disocvery of previously unannotated genes as well as correction of known genes coordinates (especially, Start codons). Almost all PrSMs which are found with a standard search with a known proteome could be also identified with SpectroGene without proteome reference.

TopFIND

Link

TopFIND is the Termini oriented protein Function Inferred Database (TopFIND), an integrated knowledge-base focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases.s.

TopPIC

Link

TopPIC (TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization) is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search. It efficiently identifies proteoforms with unexpected mutations and post-translational modifications and accurately estimates statistical significance of identifications. It uses several techniques, such indexes, spectral alignment, and a generation function method, to increase its speed, sensitivity, and accuracy.s.

YADA

Link

YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra). YADA also enables a pipeline consisting of ProLuCID and DTASelect for analyzing large-scale middle-down proteomics data.

Software – Consortium for Top-Down Proteomics (2024)

FAQs

What software is used to Analyse proteomics data? ›

Qlucore Omics Explorer lets the researcher freely examine and analyze data from proteomics experiments and generate actionable results fast and easy.

How to do top-down proteomics? ›

Top-down proteomics is a method of protein identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS.

What are the challenges of top down proteomics? ›

These challenges include protein solubility, proteome dynamic range, proteome complexity, intact protein data analysis, proteoform−function relationships, and analytical throughput.

What is top down proteomics PTM? ›

Top-down proteomics (TDP) is the study of intact proteins and their proteoforms,4,5 a term that describes the complexity of different protein forms that can arise from a single gene, introduced by truncations, post-translational modifications (PTMs), alternative splicing and/or genetic variation.

What is platform for proteomics? ›

The Broad's Proteomics Platform develops and applies advanced proteomics methods to further our understanding of disease, pathways, targets, and drug effects.

Can I use GSEA with proteomics data? ›

GSEA enables molecular signature-based statistical significance testing, which integrates protein functional category information effectively with statistical testing of functional genomics or Proteomics results.

What is a frequent disadvantage to top down? ›

Disadvantages of top-down management

Ultimately, top-down management doesn't work for everyone. It can limit creativity and slow down problem-solving, so it may not be the best choice for teams that require greater flexibility and responsiveness.

What are the disadvantages of top down process? ›

Cons of top-down management
  • Autocratic.
  • Disengaged employees.
  • Decisions based on partial information.
  • Limited innovation.
  • Slow to respond to crises (in larger organisations)
Jul 17, 2023

Why is proteomics harder than genomics? ›

After genomics and transcriptomics, proteomics is considered the next step in the study of biological systems. It is much more complicated than genomics mostly because while an organism's genome is more or less constant, the proteome differs from cell to cell and from time to time.

What is top down proteomics data analysis? ›

Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing.

Why is top down proteomics more advantageous than bottom up proteomics? ›

In the traditional Bottom Up approach, intact proteins are digested into peptides prior to introduction into the mass spectrometer where they are then detected and fragmented. In Top Down mass spectrometry, the protein is ionized directly, allowing for improved sequence coverage and detection of PTMs.

Where do I deposit proteomics data? ›

Table 1
Database NameURLProteome Xchange
Proteomics data archives
PRIDEhttps://www.ebi.ac.uk/prideX
MassIVEhttps://massive.ucsd.edu/ProteoSAFe/static/massive.jspX
JPOSThttps://repository.jpostdb.org/X
20 more rows
Dec 18, 2022

Which software is used for protein structure analysis? ›

hom*ology modeling
NameMethod
ESyPred3DTemplate detection, alignment, 3D modeling
FoldXEnergy calculations and protein design
Phyre and Phyre2Remote template detection, alignment, 3D modeling, multi-templates, ab initio
HHpredTemplate detection, alignment, 3D modeling
11 more rows

What is proteomics and proteome analysis tools? ›

Proteomics in particular analyzes changes in protein levels and can quantify individual proteins using techniques like 2D gel electrophoresis and mass spectrometry. The integration of genomics and proteomics provides a more comprehensive understanding of biological systems and is improving the drug discovery process.

What are the tools used in computational proteomics? ›

Computational Tools
  • CPTAC (Python package) Accessing and interacting with CPTAC data in python.
  • GDC. Harmonizing DNA sequences from CPTAC whole genome sequencing, whole exomes sequencing, and RNAseq using GDC pipelines.
  • PDC. ...
  • TCIA. ...
  • CDAP. ...
  • COSMO. ...
  • DREAM AI. ...
  • MassQC.

How is proteomic analysis done? ›

Mass spectrometry is a common tool for proteome analysis. Usually coupled with a liquid chromatography system, this method for protein identification relies on fragment detection and measurement, which when compared to large scale data bases can accurately identify peptide sequences present in samples.

Top Articles
Latest Posts
Article information

Author: Jerrold Considine

Last Updated:

Views: 5583

Rating: 4.8 / 5 (58 voted)

Reviews: 81% of readers found this page helpful

Author information

Name: Jerrold Considine

Birthday: 1993-11-03

Address: Suite 447 3463 Marybelle Circles, New Marlin, AL 20765

Phone: +5816749283868

Job: Sales Executive

Hobby: Air sports, Sand art, Electronics, LARPing, Baseball, Book restoration, Puzzles

Introduction: My name is Jerrold Considine, I am a combative, cheerful, encouraging, happy, enthusiastic, funny, kind person who loves writing and wants to share my knowledge and understanding with you.