Links of Interest

CIeaD MS2 Spectral Library for Plant Metabolites

• The CIeaD spectral library is  an open-access mass spectral resource containing complementary CID and EAD MS/MS spectra for 2,305 plant metabolites. They were acquired in both positive and negative ionization modes. To ensure broad cross-platform compatibility, the library is available in multiple standard formats, including .lpb, .msp, .txt, .sdf, and .mgf.
• Here please download the CIeaD Mass Spectral Library to integrate it into your in-house spectral databases for further expansion and application in your metabolomics research.

MSIonization Predictor

• This is the first machine learning-driven tool to predict optimal ionization mode (positive or negative) for small molecules. It performs binary classification using molecular structure (SMILES) as input to deliver rapid, scalable predictions with probability scores and applicability domain assessments.
• Here please find detailed instructions on using the MSIonization Predictor.

Special Opportunities for High School Students

• Florida Junior Academy of Science


• University of Florida Center for Precollegiate Education & Training


• University of Florida Student Science Training Program


• Intel Education Initiative

High Quality Proteomics Services

• University of Florida Proteomics Facility, Interdisciplinary Center for Biotechnology Research (ICBR)

2-D PolyAcrylamide Gel Electrophoresis (PAGE)

• World 2-D PAGE: Index to Databases and Services


• Proteome 2-D PAGE: Database System for Microbial Research at Max Planck Institute for Infection Biology


• Human 2-D PAGE: Danish Centre for Translational Breast Cancer Research


• 2-D PAGE Database: Swiss 2-D PAGE


• Yeast Protein Map (France): Institut de Biochimie et Génétique Cellulaires


• Yeast 2-D PAGE (Sweden): Göteborgs University

Protein Cleavage

• Mass Spectrometry Digest: Protein Prospector, University of California, San Francisco


• Peptide Mass: Expert Protein Analysis System Proteomics Server, Swiss Institute of Bioinformatics


• Mass Spectrometric Analysis: General Protein/Mass Analysis for Windows (GPMAW)

Posttranslational Modification

• Predict potential protein posttranslational modifications; find potential single amino acid substitutions in peptides: FindMod, Expert Protein Analysis System Proteomics Server, Swiss Institute of Bioinformatics


• Predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses: GlycoMod, Expert Protein Analysis System Proteomics Server, Swiss Institute of Bioinformatics


• Scansite: Massachusetts Institute of Technology


• Neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins: NetPhos Server, Center for Biological Sequence Analysis, Technical University of Denmark


• Phosphorylation database: Eucaryotic Linear Motif Resource for Functional Sites in Proteins


• Find proteins by name or keyword: PlantsP, Functional Genomics of Plant Phosphorylation, Purdue University


• Database of Protein Post Translational Modifications: Delta Mass, Association of Biomolecular Resource Facilities



 

Biomolecular Interaction

• DIP Protein Interactions


• BluePrint Biomolecular Interaction


• Mint Molecular Interaction



 

Sequence Databases

• NCBI genomes


• NCBI nr


• NCBI dbEST


• MSDB (USA)


• MSDB (Europe)


• SwissProt (Expasy)


• SwissProt (EBI)



 

Protein Identification

• MultiIdent, TagIdent and PeptIdent


• PeptideSearch


• MOWSE


• Prowl


• Protein Prospector


• MASCOT


• Lutefisk


• MassSearch


• SEQUEST


• Sherpa



 

Journals

• Journal of Proteomics


• Proteomics


• Proteomics Clinical Applications


• Journal of Proteome Research


• Molecular and Cellular Proteomics


• Proteome Science


• Current Proteomics


• Journal of Proteomics and Bioinformatics


• Human Genomics and Proteomics


• Cancer Genomics and Proteomics


• Briefings in Functional Genomics and Proteomics


• Biochimica et Biophysica Acta - Proteins and Proteomics


• Comparative Biochemistry and Physiology Part D - Genomics and Proteomics


• Proteomics Virtual Journal


• The Internet Journal of Genomics and Proteomics


• Proteomics Weekly



 

Societies and Organizations

• American Society for Mass Sepctrometry


• Association of Biomolecular Resource Facilities


• British Society for Mass Spectrometry


• The Electrophoresis Society


• The Proteome Society


• The Protein Society


• The Swiss Proteomics Society


• ASBMB


• Proteome Sciences


• Proteomics SURF


• Spectroscopy in Proteomics


• Mass Spectrometry and Biotechnology Resource


• Mass Spectrometry Web Address


• ProteinScience.com


• Large Scale Biology


• NCBI


• European Bioinformatics Institute


• Swiss Institute of Bioinformatics



 

Other Useful Links

• Protein sequence and structure prediction


• 3D-pssm


• PROSITE (Expasy)


• Chen lab Research at UF


• PMCB Program at UF


• Genetics Institute at UF