Category: proteomics

Abacus 20160720 – Extracting Spectral Counts from MS/MS Data Sets.

Abacus 20160720

:: DESCRIPTION

Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOs
  • Java

:: DOWNLOAD

Abacus 

:: MORE INFORMATION

Citation:

Proteomics. 2011 Apr;11(7):1340-5. doi: 10.1002/pmic.201000650. Epub 2011 Feb 17.
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.
Fermin D, Basrur V, Yocum AK, Nesvizhskii AI.

ProHits v4.0.3 – LIMS for Interaction Proteomics.

ProHits v4.0.3

:: DESCRIPTION

ProHits is an open source software package designed to help scientists store, search and analyze mass spectrometry data, in particular for protein-protein interaction experiments.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

ProHits

:: REQUIREMENTS

  • Linux
  • PHP
  • Apache
  • MYSQL.

:: DOWNLOAD

 ProHits

:: MORE INFORMATION

Citation:

F. Liu et al., (2010)
ProHits: an integrated software platform for mass spectrometry-based interaction proteomics.
Nat Biotech, 28:1015-7

Philosopher 4.0.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 4.0.0

:: DESCRIPTION

Philosopher provides easy access to third-party tools and custom algorithms for proteomics analysis, from database searching to functional protein reports. Philosopher is also well-equipped for open search analysis, providing extended versions of PeptideProphet and ProteinProphet for peptide validation and protein inference.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Philosopher

:: MORE INFORMATION

Citation

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI.
Philosopher: a versatile toolkit for shotgun proteomics data analysis.
Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.

MSFragger / FragPipe 16.0 – Peptide Identification in Mass Spectrometry-based Proteomics

MSFragger / FragPipe 16.0

:: DESCRIPTION

MSFragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger – an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

MSFragger / FragPipe

:: MORE INFORMATION

Citation:

Andy Kong, Felipe Leprevost, Dmitry Avtonomov, Dattatreya Mellacheruvu, Alexey Nesvizhskii.
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Nat Meth, May 2017. DOI: 10.1038/nmeth.4256

DIA-Umpire 2.2.2 – Computational Analysis pipeline for DIA Proteomics data

DIA-Umpire 2.2.2

:: DESCRIPTION

DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 DIA-Umpire

:: MORE INFORMATION

Citation:

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.
Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI.
Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255.

SRMstats 1.7 – Protein significance analysis in SRM measurements

SRMstats 1.7

:: DESCRIPTION

SRMstats is a statistical framework for protein quantification in SRM experiments based on a family of linear mixed-effects models.

::DEVELOPER

Ching-Yun (Veavi) Chang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • R package / SAS

:: DOWNLOAD

 SRMstats

:: MORE INFORMATION

Citation

Ching-Yun Chang, Paola Picotti, Ruth Huttenhain, Viola Heinzelmann-Schwarz, Marko Jovanovic, Ruedi Aebersold, Olga Vitek.
“Protein significance analysis in selected reaction monitoring (SRM) measurements.”
Mol. Cell. Proteomics. 11:M111.014662, 2012.

IDEAL-Q 1.065 – Mass Spectrometry Protein Quantitation

IDEAL-Q 1.063

:: DESCRIPTION

IDEAL-Q is an automated analysis tool for label-free quantitative proteomics. It accepts mzXML raw data format and Mascot xml and ProtXML/PepXML for identification result. IDEAL-Q uses an elution time prediction and peak alignment algorithms to quantify peptides across different LC-MS runs and increase quantitation coverage. Furthermore, the tool adopts an stringent validation step on Signal-to-noise ratio, Charge state, Isotopic distribution (SCI validation) to ensure quantitation accuracy. IDEAL-Q provides variously optional normalization tools for flexible workflow design such as addition of fractionation strategies and multiple spiked internal standards

::DEVELOPER

Computational Omics Labortary, Academia Sinica

:: SCREENSHOTS

:: REQUIREMENTS

  •  Windows

:: DOWNLOAD

 IDEAL-Q

:: MORE INFORMATION

Citation

Chih-Chiang Tsou et al. ,
“IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation”,
Molecular & Cellular Proteomics, Vol. 9, pp. 131-144, 2010.

ProtMAX – Analyzing Large Shotgun Proteomics Mass Spectrometry data sets

ProtMAX

:: DESCRIPTION

ProtMAX is a fast and robust software tool for analyzing large shotgun proteomics mass spectrometry data sets.

::DEVELOPER

Molecular Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ProtMAX

:: MORE INFORMATION

Citation:

Nat Protoc. 2013 Mar;8(3):595-601. doi: 10.1038/nprot.2013.013. Epub 2013 Feb 28.
Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments.
Egelhofer V1, Hoehenwarter W, Lyon D, Weckwerth W, Wienkoop S.

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.

LFQuant 20120114 – Label-free Quantitative Analysis Tool for LC-MS/MS Proteomics Data

LFQuant 20120114

:: DESCRIPTION

LFQuant is a new analysis tool for label-free LC-MS/MS quantitative proteomics data. It is compatible with high-resolution mass spectrometers (Thermo RAW data) and two popular database search engines (SEQUEST and MASCOT) with target-decoy search strategy.

::DEVELOPER

LFQuant team

:: SCREENSHOTS

LFQuant

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LFQuant

:: MORE INFORMATION

Citation

Proteomics. 2012 Dec;12(23-24):3475-84. doi: 10.1002/pmic.201200017.
LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.
Zhang W1, Zhang J, Xu C, Li N, Liu H, Ma J, Zhu Y, Xie H.