MS Data Miner: A web-based software tool to analyze, compare and share mass spectrometry protein identifications

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MS Data Miner : A web-based software tool to analyze, compare and share mass spectrometry protein identifications. / Dyrlund, Thomas Franck; Poulsen, Ebbe Toftgaard; Sonne-Schmidt, Carsten Scavenius; Sanggaard, Kristian W; Enghild, Jan J.

I: Proteomics, Bind 12, Nr. 18, 09.2012, s. 2792-2796.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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@article{2bc9c70c9eb541968e290ee114cc8ec3,
title = "MS Data Miner: A web-based software tool to analyze, compare and share mass spectrometry protein identifications",
abstract = "Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web-based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science) and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation-system and an automatic screenshot generation tool for Mascot-assigned spectra. In addition, a GO term analysis function and a tool for generating comparative Excel data-reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC-MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides.",
keywords = "Bioinformatics, Distiller, Mascot, MS Analysis, Protein Identification, ProteinPilot",
author = "Dyrlund, {Thomas Franck} and Poulsen, {Ebbe Toftgaard} and Sonne-Schmidt, {Carsten Scavenius} and Sanggaard, {Kristian W} and Enghild, {Jan J}",
note = "{\circledC} 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.",
year = "2012",
month = "9",
doi = "10.1002/pmic.201200109",
language = "English",
volume = "12",
pages = "2792--2796",
journal = "Proteomics",
issn = "1615-9853",
publisher = "Wiley - V C H Verlag GmbH & Co. KGaA",
number = "18",

}

RIS

TY - JOUR

T1 - MS Data Miner

T2 - A web-based software tool to analyze, compare and share mass spectrometry protein identifications

AU - Dyrlund, Thomas Franck

AU - Poulsen, Ebbe Toftgaard

AU - Sonne-Schmidt, Carsten Scavenius

AU - Sanggaard, Kristian W

AU - Enghild, Jan J

N1 - © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PY - 2012/9

Y1 - 2012/9

N2 - Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web-based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science) and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation-system and an automatic screenshot generation tool for Mascot-assigned spectra. In addition, a GO term analysis function and a tool for generating comparative Excel data-reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC-MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides.

AB - Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web-based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science) and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation-system and an automatic screenshot generation tool for Mascot-assigned spectra. In addition, a GO term analysis function and a tool for generating comparative Excel data-reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC-MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides.

KW - Bioinformatics

KW - Distiller

KW - Mascot

KW - MS Analysis

KW - Protein Identification

KW - ProteinPilot

U2 - 10.1002/pmic.201200109

DO - 10.1002/pmic.201200109

M3 - Journal article

C2 - 22833312

VL - 12

SP - 2792

EP - 2796

JO - Proteomics

JF - Proteomics

SN - 1615-9853

IS - 18

ER -