myProMS 3.9.3 – Management, Validation and Interpretation of MS-based Proteomic data

myProMS 3.9.3

:: DESCRIPTION

myProMS is a comprehensive bioinformatics environment (database and web server) for management of Mass Spectrometry (MS) protein identification data generated by database-search engines such as Mascot or Sequest. Multiple functionalities are available to mine, validate and interpret the data from both MS and biological point of views. In particular, biological interpretation of the results is facilitated through the use of sophisticated data comparison modules, annotation enrichments and links to external resources. myProMS was designed to optimize data access and sharing during collaboration between users with complementary expertises; typically MS experts and biologists.

::DEVELOPER

Institut Curie, Bioinformatics Core Facility

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  myProMS

:: MORE INFORMATION

Citation

Poullet P, Carpentier S, Barillot E.
myProMS, a web server for management and validation of mass spectrometry-based proteomic data.
Proteomics. 2007, 7 (15):2553-6.

ProMS – Proteome Analysis using Mass Spectrometry

ProMS

:: DESCRIPTION

ProMS (Proteome Analysis using Mass Spectrometry) is a Web Server for Validation and Manipulation of Mass Spectrometry-based Proteomics data.

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • WebServer
  • MySQL

:: DOWNLOAD

 ProMS

:: MORE INFORMATION

Proteios 2.19.0 – Multi-user Platform for Analysis and Management of Proteomics data

Proteios 2.19.0

:: DESCRIPTION

Proteios SE (or ProSE) is meant to be installed on a local server in a proteomics laboratory.

::DEVELOPER

Jari Häkkinen @ Lund University

:: SCREENSHOTS

Proteios

:: REQUIREMENTS

:: DOWNLOAD

  Proteios

:: MORE INFORMATION

Citation

J Proteome Res. 2009 Jun;8(6):3037-43. doi: 10.1021/pr900189c.
The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data.
Häkkinen J, Vincic G, Månsson O, Wårell K, Levander F.

TopPIC 1.5 – TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization

TopPIC 1.5

:: DESCRIPTION

TopPIC is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search.

::DEVELOPER

TopPIC team

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 TopPIC

:: MORE INFORMATION

Citation:

TopPIC: A software tool for top-down mass spectrometry-based proteoform identification and characterization.
Kou Q, Xun L, Liu X.
Bioinformatics. 2016 Jul 16. pii: btw398.

Protein identification using top-down spectra.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA.
Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524.

ProteoSAFe 1.2.6 – Proteomics Environment

ProteoSAFe 1.2.6

:: DESCRIPTION

ProteoSAFe is a Proteomics Environment which is Scalable in utilizing distributed computing, Accessible via reconfigurable, easy-to-learn user interfaces, and Flexible in tool chaining.

::DEVELOPER

To-ju Huang (t3huang@ucsd.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ProteoSAFe

:: MORE INFORMATION

InsPecT 20120109 – Proteomics Search Toolkit

InsPecT 20120109

:: DESCRIPTION

Inspect is a general purpose database search algorithm, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, Inspect implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.

::DEVELOPER

Natalie Castellana [ncastell(at)cs.ucsd.edu]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  InsPecT

:: MORE INFORMATION

Citation:

InsPecT: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra.
Stephen Tanner, Hongjun Shu, Ari Frank, Ling-Chi Wang, Ebrahim Zandi, Marc Mumby, Pavel A. Pevzner, and Vineet Bafna.
Anal Chem. 2005 Jul 15;77(14):4626-39

pFind Studio 2.8.8 – Mass Spectrometry-based Proteomics

pFind Studio 2.8.8

:: DESCRIPTION

pFind Studio is a computational solution for mass spectrometry-based proteomics. pFind Studio includes pFind, pBuild, pLabel, pXtract, pParse and pScan

pXtract creates .DTA .MGF and .MS2 input files directly from Thermo Scientific .raw LC-MS/MS data files.

pParse is a software dedicated to recalibrate the monoisotopic of precursors in MS/MS spectra datasets assigned by mass spectrometry

pFind is a search engine for peptide and protein identification via tandem mass spectrometry.

pNovo+ is a de novo peptide sequencing algorithm using complementary HCD and ETD tandem mass spectra.

pBuild is a tool that can compare several search engines’ results and combine them together. The latest version, pBuild v2.0, can process the search results of pFind, SEQUEST and Mascot.

pQuant is the software for quantitative proteomics, evaluates the accuracy of caluculated peptide and protein ratios.

pLabel is a spectra labeling tool that can visualize the global- and local-view peptide-spectrum matches, given the results of pFind or any other search engines. pLabel can label both CID and ETD spectra, and implement the manual de novo sequencing.

pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.

pScan is a flexible tool that helps biologists to preprocess protein sequence databases in proteomics research.

pCluster is a software tool aiming at detecting protein modifications independent of sequence databases by tandem mass spectral clustering.

pMatch is a spectral library search tool, which is deliberately designed for the open search mode.

::DEVELOPER

Bioinformatics group, Institute of Computing Technology, Chinese Academy of Sciences

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 pFind Studio

:: MORE INFORMATION

Citation

Rapid Communications in Mass Spectrometry, 21,2985-2991,2007.
pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry.
Le-Heng Wang, De-Quan Li, Yan Fu, Hai-Peng Wang, Jing-Fen Zhang, Zuo-Fei Yuan,Rui-Xiang Sun, Rong Zeng, Si-Min He, Wen Gao.

STRAP 1.5 – Software Tool for Rapid Annotation of Proteins

STRAP 1.5

:: DESCRIPTION

STRAP, the Software Tool for Rapid Annotation of Proteins, saves you time by automatically annotating a protein list with information that helps you meaningfully interpret your mass spectrometry data.

::DEVELOPER

Cardiovascular Proteomics Center ,BU School of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 STRAP

:: MORE INFORMATION

Citation

Bhatia VN, Perlman DH, Costello CE, McComb ME.
Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.
Analytical Chemistry 2009, 81 (23), 9819-23.

GoMiner Build454- Resource for Biological Interpretation of Genomic and Proteomic data

GoMiner Build454

:: DESCRIPTION

GoMiner organizes and allows the visualization of large sets of genes based on Gene Ontology classifications.GoMiner is a tool for biological interpretation of ‘omic’ data – including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question

::DEVELOPER

GoMiner Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

 GoMiner

:: MORE INFORMATION

Citation:

Barry R Zeeberg et al.
GoMiner: a resource for biological interpretation of genomic and proteomic data
Genome Biology 2003, 4:R28

DiagnoProt 1.4 – Discovery of new Molecules by Mass Spectrometry

DiagnoProt 1.4

:: DESCRIPTION

DiagnoProt is a tool that finds discriminative mass spectra among different biological conditions and ultimately performs spectral profiling classification of unknown conditions by comparing sets of tandem mass spectra (MS/MS).

::DEVELOPER

Laboratory for Computational and Strucutural Proteomics – Fiocruz

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • The .NET framework

:: DOWNLOAD

DiagnoProt 

:: MORE INFORMATION

Citation

Silva ARF, Lima DB, Leyva A, Duran R, Batthyany C, Aquino PF, Leal JC, Rodriguez JE, Domont GB, Santos MDM, Chamot-Rooke J, Barbosa VC, Carvalho PC.
DiagnoProt: a tool for discovery of new molecules by mass spectrometry.
Bioinformatics. 2017 Jun 15;33(12):1883-1885. doi: 10.1093/bioinformatics/btx093. PMID: 28186229.