LC-IMS-MS Feature Finder v2.2.6487 – Detecting Multidimensional Liquid Chromatography, Ion Mobility and Mass Spectrometry features

LC-IMS-MS Feature Finder v2.2.6487

:: DESCRIPTION

LC-IMS-MS Feature Finder is a command line software application that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time, and ion mobility drift time values.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
Microsoft NET Framework 2.0

:: DOWNLOAD

LC-IMS-MS Feature Finder

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2804-5. doi: 10.1093/bioinformatics/btt465. Epub 2013 Sep 5.
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.
Crowell KL1, Slysz GW, Baker ES, LaMarche BL, Monroe ME, Ibrahim YM, Payne SH, Anderson GA, Smith RD.

NITPICK 2.0 – Peak Identification for Mass Spectrometry Data

NITPICK 2.0

:: DESCRIPTION

NITPICK is a Non-greedy, Iterative Template-based peak PICKer that deconvolves complex overlapping isotope distributions in multicomponent mass spectra.

::DEVELOPER

Image Analysis and Learning Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

NITPICK

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Aug 28;9:355. doi: 10.1186/1471-2105-9-355.
NITPICK: peak identification for mass spectrometry data.
Renard BY1, Kirchner M, Steen H, Steen JA, Hamprecht FA.

pLSA – Probabilistic Latent Semantic Analysis of Imaging Mass Spectrometry Data

pLSA

:: DESCRIPTION

pLSA contains MATLAB code to perform a probabilistic Latent Semantic Analysis of Imaging Mass Spectrometry Data. In contrast to other unsupervised methods like Principal Component Analysis or Independent Component Analysis this method accounts for the non-negativity of mass spectra.

::DEVELOPER

Image Analysis and Learning Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
MatLab

:: DOWNLOAD

pLSA

:: MORE INFORMATION

Citation

Anal Chem. 2008 Dec 15;80(24):9649-58. doi: 10.1021/ac801303x.
Concise representation of mass spectrometry images by probabilistic latent semantic analysis.
Hanselmann M1, Kirchner M, Renard BY, Amstalden ER, Glunde K, Heeren RM, Hamprecht FA.

PyMsXML 0.5.4 – Convert Vendor Specific Mass Spectrometry file formats to open XML file formats

PyMsXML 0.5.4

:: DESCRIPTION

PyMsXML is a python script for converting vendor specific mass spectrometry data files for Applied Biosystems’ Q-Star, 4700, 4800, Mariner, and Voyager mass spectrometers from their raw binary form, to either of the emerging XML file formats for mass spectra: mzXML, from the Sashimi Glossolalia project of the Institute for Systems Biology (ISB); and mzData, from the Proteome Standardization Initiative (PSI) project of the Human Proteome Organization (HUPO).

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Python

:: DOWNLOAD

PyMsXML

:: MORE INFORMATION

EXIMS 20141021 – EXploring Imaging Mass Spectrometry data

EXIMS 20141021

:: DESCRIPTION

EXIMS presents an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data.

::DEVELOPER

EXIMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Window
MatLab

:: DOWNLOAD

EXIMS

:: MORE INFORMATION

Citation

EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data.
Wijetunge CD, Saeed I, Boughton BA, Spraggins JM, Caprioli RM, Bacic A, Roessner U, Halgamuge SK.
Bioinformatics. 2015 Jun 10. pii: btv356.

PRIDE Converter 2.5.7 – Converts Mass Spectrometry Data into PRIDE XML

PRIDE Converter 2.5.7

:: DESCRIPTION

PRIDE Converter 2 converts mass spectrometry data from most common data formats into valid PRIDE XML for submission to the publicly available PRIDE database. It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service.

::DEVELOPER

PRIDE Converter Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

PRIDE Converter

:: MORE INFORMATION

Citation

Barsnes et. al:
PRIDE Converter: making proteomics data-sharing easy
Nat Biotechnol. 2009 Jul;27(7):598-9.

Cote RG & Griss J, et al.,
The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Mol Cell Proteomics. 2012 Sep 4.

Mass++ Ver.4 beta – Analysis Tool for Mass Spectrometry

Mass++ Ver.4 beta

:: DESCRIPTION

Mass++ is freeware for mass spectrometry data analysis developed and released by our FIRST ms³d project. It can load data files of various mass spectrometers, display data with various kinds of views, and analyze data by various kinds of analysis functions.

::DEVELOPER

Koichi Tanaka Laboratory of Advanced Science and Technology

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Mass++

:: MORE INFORMATION

Citation:

J Proteome Res. 2014 Jul 7.
Mass++: A Visualization and Analysis Tool for Mass Spectrometry.
Tanaka S1, Fujita Y, Parry HE, Yoshizawa AC, Morimoto K, Murase M, Yamada Y, Yao J, Utsunomiya SI, Kajihara S, Fukuda M, Ikawa M, Tabata T, Takahashi K, Aoshima K, Nihei Y, Nishioka T, Oda Y, Tanaka K.

ProSight Lite 1.4.7 – Analyze Top-down Mass Spectrometry data

ProSight Lite 1.4.7

:: DESCRIPTION

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

::DEVELOPER

Proteomics Center of Excellence

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Visual C++ 2013 Runtime Libraries (x86)
Microsoft .NET Framework 4.5.1 (x86 and x64)

:: DOWNLOAD

ProSight Lite

:: MORE INFORMATION

Citation

Proteomics. 2014 Dec 12. doi: 10.1002/pmic.201400313. [Epub ahead of print]
ProSight Lite: Graphical software to analyze top-down mass spectrometry data.
Fellers RT1, Greer JB, Early BP, Yu X, LeDuc RD, Kelleher NL, Thomas PM.

SIRIUS 4.9.3 – Identification of Metabolites using single and Tandem Mass Spectrometry

Sirius 4.9.3

:: DESCRIPTION

Sirius ,(Sum formula Identification by Ranking Isotope patterns Using mass Spectrometry) a new java-based software framework for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. Sirius² deduces molecular formulas of small compounds by ranking isotope patterns from mass spectra of high resolution. Sirius² further analyses the fragmentation pattern of a compound resulting in hypothetical fragmentation trees. It allows for automated and high-throughput analysis of small-compound MS data beyond elemental composition without requiring compound structures or a mass spectral database.

::DEVELOPER

Lehrstuhl Bioinformatik Jena

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

Sirius

:: MORE INFORMATION

Citation:

SIRIUS: decomposing isotope patterns for metabolite identification
Sebastian B?cker, Matthias C. Letzel, Zsuzsanna Lipták and Anton Pervukhin
Bioinformatics (2009) 25 (2): 218-224

SpectroGene 1.0 – Genome Annotation using Top-down Mass Spectrometry

SpectroGene 1.0

:: DESCRIPTION

SpectroGene is a tool for top-down protein identification using unannotated bacterial genome.

::DEVELOPER

Mikhail Kolmogorov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

SpectroGene

:: MORE INFORMATION

Citation:

SpectroGene: a tool for proteogenomic annotations using top-down spectra.
Kolmogorov M, Liu X, Pevzner PA.
J Proteome Res. 2015 Dec 2.