CHOP-Penn Proteomics Core Tools and Fees

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  • Sequence database search engines: Proteome Discoverer, SEQUEST, Mascot, X!Tandem, MaxQuant, trans-proteomic pipeline (TPP)
  • Visualization and data analysis: Perseus, Scaffold and Skyline, TPP
  • Bioinformatics
  • R
  • Perl
  • UniProtKB: The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.
  • Human Proteome Map: The Human Proteome Map (HPM) portal is an interactive resource to the scientific community by integrating the massive peptide sequencing result from the draft map of the human proteome project.
  • PeptideAtlas: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
  • The Human Protein Atlas: a program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology.
  • Unimod: a database for protein modifications by mass spectrometry searchable by mass, atomic composition, name, description, and more.
  • ExPASy - UniProt Knowledgebase: Swiss-Prot and TrEMBL: UniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB). It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.
  • GPMDB Proteome Database: was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.
  • bioDBnet: db2db: biological DataBase network is an application integrating a vast number of biological databases including Gene, UniProt, Ensembl, GO, Affy, RefSeq etc. The databases are created by downloading data from various public resources. They are formatted and maintained in a relational structure at the Advanced Biomedical Computing Center (ABCC). db2db allows for conversions of identifiers from one database to other database identifiers or annotations.
  • NIST Mass Spectrometry Tools: The NIST Mass Spectrometry Data Center, a Group in the Biomolecular Measurement Division (BMD), develops evaluated mass spectral libraries and provides related software tools. These products are intended to assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry) as well as gas phase retention indices for GC.
  • Proteome Xchange: The ProteomeXchange Consortium was established to provide globally coordinated standard data submission and dissemination pipelines involving the main proteomics repositories, and to encourage open data policies in the field.
  • SPC Proteomics Tools: Seattle Proteome Center (SPC) - Proteomics Tools. NHLBI Proteomics Center at the Institute for Systems Biology
  • MascotDatabaseSearch: Matrix Science for identification, characterization and quantitation of proteins using mass spectrometry data. Here, you can learn more about the tools developed by Matrix Science to get the best out of your data, whatever your chosen instrument.
  • Proteome Software - Scaffold: Visualize and validate complex MS/MS proteomics experiments
  • MaxQuant: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.
  • Perseus: The Perseus software platform supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing.
  • Skyline: Skyline is a freely-available and open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), Data Independent Acquisition (DIA/SWATH) and DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.
  • DAVID Functional Annotation Bioinformatics: The Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.8 comprises a full Knowledgebase update to the sixth version of our original web-accessible programs. DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
  • motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set.
  • Human Microbiome Project DACC - HMRGD he HMP plans to sequence, or collect from associated efforts, a total of 3000 reference genomes isolated from human body sites. The majority of these will be sequenced only to a high-quality draft stage. Metadata about current, completed and targeted reference genome projects can be found in the Project Catalog.
  • Functional Glycomics Gateway: The Functional Glycomics Gateway is a comprehensive resource for functional glycomics research brought to you by the Consortium for Functional Glycomics (CFG). Use this site to access our extensive databases, to request CFG resources and services, and to visit our archives of research publications and editorials.
  • IDCalc -- Isotope Distribution Calculator: IDCalc was developed to provide a simple way to view the expected isotope distribution for biological molecules measured by mass spectrometry. The program also includes the the ability to consider enriched stable isotopes. Input is either as a peptide sequence or an elemental composition through the graphical user interface.
  • IsoPro: is the original mass spectral isotopic distribution simulator for Windows. It is now available as freeware. IsoPro is based on the Yergey algorithm
  • ProteinProspector: A rich variety of Proteomics tools for mining sequence databases

In conjunction with Mass Spectrometry experiments.

  • ABRF: Association of Biomolecular Resource Facilities
  • ASMS: American Society for Mass Spectrometry