Literature DB >> 22833312

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

Thomas F Dyrlund1, Ebbe T Poulsen, Carsten Scavenius, Kristian W Sanggaard, Jan J Enghild.   

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

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Year:  2012        PMID： 22833312     DOI： 10.1002/pmic.201200109

Source DB:  PubMed          Journal:  Proteomics        ISSN： 1615-9853            Impact factor:   3.984


  27 in total

1.  A splice variant of the human ion channel TRPM2 modulates neuroblastoma tumor growth through hypoxia-inducible factor (HIF)-1/2α.

Authors:  Shu-jen Chen; Nicholas E Hoffman; Santhanam Shanmughapriya; Lei Bao; Kerry Keefer; Kathleen Conrad; Salim Merali; Yoshinori Takahashi; Thomas Abraham; Iwona Hirschler-Laszkiewicz; JuFang Wang; Xue-Qian Zhang; Jianliang Song; Carlos Barrero; Yuguang Shi; Yuka Imamura Kawasawa; Michael Bayerl; Tianyu Sun; Mustafa Barbour; Hong-Gang Wang; Muniswamy Madesh; Joseph Y Cheung; Barbara A Miller
Journal:  J Biol Chem       Date:  2014-11-12       Impact factor: 5.157

2.  Coagulation factor XIIIa substrates in human plasma: identification and incorporation into the clot.

Authors:  Camilla Lund Nikolajsen; Thomas F Dyrlund; Ebbe Toftgaard Poulsen; Jan J Enghild; Carsten Scavenius
Journal:  J Biol Chem       Date:  2014-01-17       Impact factor: 5.157

3.  The protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms.

Authors:  Waltraud X Schulze; Kristian W Sanggaard; Ines Kreuzer; Anders D Knudsen; Felix Bemm; Ida B Thøgersen; Andrea Bräutigam; Line R Thomsen; Simon Schliesky; Thomas F Dyrlund; Maria Escalante-Perez; Dirk Becker; Jörg Schultz; Henrik Karring; Andreas Weber; Peter Højrup; Rainer Hedrich; Jan J Enghild
Journal:  Mol Cell Proteomics       Date:  2012-08-12       Impact factor: 5.911

Review 4.  The Human Eye Proteome Project: perspectives on an emerging proteome.

Authors:  Richard D Semba; Jan J Enghild; Vidya Venkatraman; Thomas F Dyrlund; Jennifer E Van Eyk
Journal:  Proteomics       Date:  2013-08       Impact factor: 3.984

5.  Proteomic profiling of TGFBI-null mouse corneas reveals only minor changes in matrix composition supportive of TGFBI knockdown as therapy against TGFBI-linked corneal dystrophies.

Authors:  Ebbe Toftgaard Poulsen; Kasper Runager; Nadia Sukusu Nielsen; Marie V Lukassen; Karen Thomsen; Paige Snider; Olga Simmons; Henrik Vorum; Simon J Conway; Jan J Enghild
Journal:  FEBS J       Date:  2017-11-23       Impact factor: 5.542

6.  TRPM2 channels protect against cardiac ischemia-reperfusion injury: role of mitochondria.

Authors:  Barbara A Miller; Nicholas E Hoffman; Salim Merali; Xue-Qian Zhang; JuFang Wang; Sudarsan Rajan; Santhanam Shanmughapriya; Erhe Gao; Carlos A Barrero; Karthik Mallilankaraman; Jianliang Song; Tongda Gu; Iwona Hirschler-Laszkiewicz; Walter J Koch; Arthur M Feldman; Muniswamy Madesh; Joseph Y Cheung
Journal:  J Biol Chem       Date:  2014-02-03       Impact factor: 5.157

7.  How Glycosaminoglycans Promote Fibrillation of Salmon Calcitonin.

Authors:  Kirsten Gade Malmos; Morten Bjerring; Christian Moestrup Jessen; Erik Holm Toustrup Nielsen; Ebbe T Poulsen; Gunna Christiansen; Thomas Vosegaard; Troels Skrydstrup; Jan J Enghild; Jan Skov Pedersen; Daniel E Otzen
Journal:  J Biol Chem       Date:  2016-06-08       Impact factor: 5.157

8.  Insight into the Protein Composition of Immunoglobulin Light Chain Deposits of Eyelid, Orbital and Conjunctival Amyloidosis.

Authors:  Nadia Sukusu Nielsen; Ebbe Toftgaard Poulsen; Gordon K Klintworth; Jan J Enghild
Journal:  J Proteomics Bioinform       Date:  2014-04-21

9.  Comparison of two phenotypically distinct lattice corneal dystrophies caused by mutations in the transforming growth factor beta induced (TGFBI) gene.

Authors:  Ebbe Toftgaard Poulsen; Kasper Runager; Michael W Risør; Thomas F Dyrlund; Carsten Scavenius; Henrik Karring; Jeppe Praetorius; Henrik Vorum; Daniel E Otzen; Gordon K Klintworth; Jan J Enghild
Journal:  Proteomics Clin Appl       Date:  2014-02-16       Impact factor: 3.494

10.  SILAC-Based Mass Spectrometry Analysis Reveals That Epibrassinolide Induces Apoptosis via Activating Endoplasmic Reticulum Stress in Prostate Cancer Cells.

Authors:  Pinar Obakan; Carlos Barrero; Ajda Coker-Gurkan; Elif Damla Arisan; Salim Merali; Narcin Palavan-Unsal
Journal:  PLoS One       Date:  2015-09-09       Impact factor: 3.240
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