ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry

ProSight PTM 2.0 (http://prosightptm2.scs.uiuc.edu) is the next generation of the ProSight PTM web-based system for the identification and characterization of proteins using top down tandem mass spectrometry. It introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing). Furthermore, it supports data import and export for local analysis and collaboration.

[1]  Scott A McLuckey,et al.  Gas-phase concentration, purification, and identification of whole proteins from complex mixtures. , 2002, Journal of the American Chemical Society.

[2]  Yong-Bin Kim,et al.  ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry , 2004, Nucleic Acids Res..

[3]  M. Mann,et al.  4. Proteomic Analysis of Posttranslational Modifications , 2013 .

[4]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[5]  W. Pearson,et al.  Current Protocols in Bioinformatics , 2002 .

[6]  Neil L Kelleher,et al.  Shotgun annotation of histone modifications: a new approach for streamlined characterization of proteins by top down mass spectrometry. , 2004, Journal of the American Chemical Society.

[7]  Elizabeth M. Smigielski,et al.  dbSNP: a database of single nucleotide polymorphisms , 2000, Nucleic Acids Res..

[8]  J. Fenn,et al.  Ion formation from charged droplets: Roles of geometry, energy, and time , 1993, Journal of the American Society for Mass Spectrometry.

[9]  F. McLafferty,et al.  Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process , 1998 .

[10]  Neil L Kelleher,et al.  Precise and Parallel Characterization of Coding Polymorphisms, Alternative Splicing, and Modifications in Human Proteins by Mass Spectrometry*S , 2005, Molecular & Cellular Proteomics.

[11]  N. Kelleher,et al.  Fourier‐transform mass spectrometry for automated fragmentation and identification of 5‐20 kDa proteins in mixtures , 2002, Electrophoresis.

[12]  Neil L Kelleher,et al.  Using ProSight PTM and related tools for targeted protein identification and characterization with high mass accuracy tandem MS data. , 2007, Current protocols in bioinformatics.

[13]  大房 健.  基礎講座 電気泳動(Electrophoresis) , 2005 .

[14]  M. Mann,et al.  Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.

[15]  Neil L. Kelleher,et al.  Informatics and multiplexing of intact protein identification in bacteria and the archaea , 2001, Nature Biotechnology.

[16]  David Haussler,et al.  LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources , 2005, Bioinform..

[17]  Robert M. Stephens,et al.  The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database , 2001, Nucleic Acids Res..

[18]  M. Senko,et al.  New and automated MSn approaches for top-down identification of modified proteins , 2005, Journal of the American Society for Mass Spectrometry.

[19]  J R Yates,et al.  Analysis of the microbial proteome. , 2000, Current opinion in microbiology.

[20]  F. McLafferty,et al.  High-resolution electrospray mass spectra of large molecules , 1991 .

[21]  A G Marshall,et al.  A high-performance modular data system for Fourier transform ion cyclotron resonance mass spectrometry. , 1996, Rapid communications in mass spectrometry : RCM.

[22]  F. McLafferty,et al.  Automated reduction and interpretation of , 2000, Journal of the American Society for Mass Spectrometry.

[23]  M. Wilm,et al.  Error-tolerant identification of peptides in sequence databases by peptide sequence tags. , 1994, Analytical chemistry.