Resources of NHLBI Proteomics Centers

What is this?

This is a preliminary reports to collect available resources developed at all NHLBI proteomics centers. The objective is to classify resource along the following four categories: protocol, database, software, and standard. In addition, another category - others - is created for events and courses and other useful information. The last category RSS is the result of if any of these centers have provide RSS feed.

Vascular Endothelial Cell Isolation Protocol

Center: Medical College of Wisconsin

URI: http://proteomics.mcw.edu/components/models/methods.jsp

Resource: http://proteomics.mcw.edu/components/models/Endothelial-Cell-Isolation.doc.

Stimulator Implantation for TA muscle

Center: Medical College of Wisconsin

URI: http://proteomics.mcw.edu/components/models/methods.jsp

Resource: http://proteomics.mcw.edu/components/models/Stimulator-Implantation.doc.

Culture of Vascular Endothelial Cells Intended for Hypoxia/Matrigel^TM

Center: Medical College of Wisconsin

URI: http://proteomics.mcw.edu/components/models/methods.jsp

Resource: http://proteomics.mcw.edu/components/models/Culture-VECsI-Mg-Hx.doc.

Culture of Electrically Stimulated Vascular Endothelial Cells

Center: Medical College of Wisconsin

URI: http://proteomics.mcw.edu/components/models/methods.jsp

Resource: http://proteomics.mcw.edu/components/models/Culture-Stimulated.doc.

Acid Cleavable ICAT Labeling Protocol

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Acid%20Cleavable%20ICAT%20Labelling%20Protocol.pdf

Orig ICAT (hydrogen/deuterium) Labeling Procedure

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Orig%20ICAT%20Labelling%20Procedure.pdf

Protocol for Making 500 mg of Photo-Beads

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Protocol%20for%20Making%20500%20mg%20of%20Photo-Beads.pdf

Protocol for Labeling with d0d6-GABA Photo-Beads

Center Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Protocol%20for%20Labelling%20with%20d0d6-GABA%20Photo-Beads.pdf

Profiling ICAT Label Procedure for Budding Yeast Whole Proteome

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Profiling%20ICAT%20Label%20Procedure%20for%20Budding%20Yeast%20Whole%20Proteome.pdf

Stable Isotope Tagging of Affinity Purified Complexes

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Stable%20Isotope%20Tagging%20of%20Affinity%20Purified%20Complexes.pdf

Mammalian TAP-Tagging Technique

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Mammalian%20TAP%20protocols.pdf

RNA interference in THP

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/RNAi-THP.pdf

Trypsin Digestion Procedures

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Trypsin%20Digestion%20Procedures.pdf

Cation Exchange Procedure for ICAT Samples

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Cation%20Exchange%20Procedure%20for%20ICAT%20Samples.pdf

Packing a Reversed-Phase Microcapillary Column

Center: Institute of System Biology

URI: http://www.proteomecenter.org/protocols/Packing%20a%20Reversed-Phase%20Microcapillary%20Column.pdf

Phospho-Flow Protocol

Center: Stanford

URI: http://proteomics.stanford.edu/nolan/phospho_flow.html

Description: Flow cytometryhas become an indispensable tool in clinical and basic immunological research due to its ability to distinguish subsets in heterogeneous populations of cells. Recently, major advances have been made in both flow cytometry machinery and applications, expanding the number of possible simultaneous analysis parameters to thirteen or more [1,2]. With more parameters available, researchers have begun to identify more well-defined and biologically interesting subsets of lymphocytes in human and murine samples based upon surface epitope staining. Although surface staining may be an effective means of characterizing cells, it does not provide information about the functional responses of those cells to stimuli that are immediately reflective of intracellular events. Even in cases where the marker used is a cytokine receptor or receptor tyrosine kinase, levels of the antigen do not always correlate with cellular response to the specific ligand [3]. Therefore, methods have been developed to characterize cells by levels of intracellular epitopes: cytokines, DNA, mRNA, enzymes, hormone receptors, cell cycle proteins, and of particular interest to this review, phosphorylated signaling molecules.

Antigen Array

Center: Stanford

URI: http://proteomics.stanford.edu/robinson/protocol.html

Isoelectric Focusing - 11cm strips (Criterion Gels)

Center: UTMB

URI: http://www.bioinfo.utmb.edu/proteomics/NHLBI/Isoeletric.pdf

SDS PAGE - 11cm IPG Strips

Center: UTMB

URI: http://www.bioinfo.utmb.edu/proteomics/NHLBI/SDSPage.pdf

Gel Fixation and SYPRO Ruby Staining

Center: UTMB

URI: http://www.bioinfo.utmb.edu/proteomics/NHLBI/Gel_Fixation.pdf

Imaging Gels Stained with SYPRO Ruby

Center: UTMB

URI: http://www.bioinfo.utmb.edu/proteomics/NHLBI/Imaging_Gels.pdf

Whole Nuclear Extract

Center: UTMB

URI: http://www.bioinfo.utmb.edu/proteomics/NHLBI/Whole_Nuclear_Extract.pdf

Nuclear Protein preparation - High salt and post nuclear extract

Center: UTMB

URI: http://www.bioinfo.utmb.edu/proteomics/NHLBI/Nuclear_Protein_preparation.pdf

Proteome Database

Institute: Johns Hopkins University

URI: http://proteomics.jhu.edu/dl/pathidb.php

Description: The JHU Proteomic Database is used to store raw, processed and final proteomic data from a large number of methods, technologies, clinical and physiological studies from cardiac studies through the National Heart, Lung and Blood Institute (NHLBI). This database will be used to mine information about proteins, protein patterns and post translational modifications (PTMs) and the associated methods and technologies. The data will be used to help create "protein profiles" to determine not only if disease is present, but the severity and progression of disease in the patient.

Human Protein Reference Database

Institute: Johns Hopkins University

URI: http://www.hprd.org/

Description: The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.

BUPID (Boston University Protein Identifier)

Center: Boston University

URI: http://fincher.bu.edu/tww/BUPID/

Description: Several software programs have now been developed for MS data interpretation by querying a sequence database with peptide masses obtained from the MS experiment. We present results from a new search algorithm; Boston University Protein Identifier (BUPID), a robust and accurate statistical model for protein identification using MS data. The algorithm offers a number of new features in comparison to presently used algorithms: 1. Using log-likelihood ratio as scoring function, the algorithm can better distinguish correctly assigned peptides from incorrect assignments. 2. Matching peaks with a background-dependent threshold offers more flexibility and accuracy than the traditional mass error window. 3. The statistical model is shown to provide equivalent/ better results in comparison to other models. (from http://www.bumc.bu.edu/www/busm/cap/documents/ASMS2005Tong.pdf )

PepID: Protein Identification by Peptide Clustering

Center: Medical College of Wisconsin

URI: http://proteomics.mcw.edu/pepid/index.jsp .

Description: N/A.

DeNovoID: Protein Identification using de novo Peptide Sequence Data

Center: Medical College of Wisconsin

URI: http://proteomics.mcw.edu/denovoid/index.jsp .

Description: N/A.

ProMoST: Protein Modification Screening Tool

Center: Medical College of Wisconsin

URI: http://proteomics.mcw.edu/promost/index.jsp .

Description: Program to calculate accurate MWT and pI values from proteins.

AGML Central

Center: Medical University of South Carolina

URI: http://www.agml.org

Description: AGML Central is a central location that includes tools for the creation of AGML (Annotated Gel Markup Language, see research article at BMC Bioinformatics) XML document to analysis tools to analyse the 2-D Gel Electrophoretic data representeed in the AGML format. AGML Central includes tool to convert native formats from PDQUEST, PHORETIX and Melanie to the AGML format. Additionally the MI2DG web page records the protocol used in the creation of the 2-D Gel and this information is included in the AGML instance document. AGML instance document is then subjected to the analysis using the MATLAB and the results are accessible through the analysis page. All the these steps are done automatically once the native files are uploaded throught the upload page. Schema page describes the AGML XML in more detail and also gives other links to other projects at Bioinformatics@MUSC.

WebNN

Center: Medical University of South Carolina

URI: https://bioinformatics.musc.edu/webnn/

Description: data management and analysis of 2D gel electrophoresis proteomics screening.

Protein Identification from Spectra of Intact Proteins (PISIP)

Center: Medical University of South Carolina

URI: http://s05.135can.musc.edu/psearch/search.html

Description: Protein Identification from Spectra of Intact Proteins performs database searches using tandem mass spectra obtained from the fragmentation of intact proteins. The search algorithm matches observed masses against a database of predicted fragment masses and scores proteins which match a minimum number of fragment masses. Enter your observed masses in the text area to the right and select your search parameters on the left. When using the Intensity-weighted scoring enter intensities adjacent to the associated mass. Submit your search by pressing the "Search" button below.

Charleston Core Wiff File Converter (CCWiffer)

Center: Administrative Center and Medical University of South Carolina

URI: http://www.charlestoncore.org/tools/ccwiffer.html

Description: CCWiffer is a short name for "Charleston Core Wiff Converter". It is a software designed to help proteomic users converting Mass Spectrometry (MS) data stored in proprietary Wiff format into a community standard XML-based format.

Trans-Proteomic Pipeline (TPP)

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/TPP.php

Description: The TPP includes all steps of the ISB MS/MS analysis pipeline after results of database search: Peptide validation, Peptide quantitation, Protein identification, and Protein quantitation. XML-based, the TPP is easily extensible to additional search engines and analysis modules.

PeptideProphetTM Package

Center: Institute of System Biology

URI: PeptideProphet^TM Package

Description: A robust and accurate statistical approach, based on the expectation maximization algorithm, for validation of peptide identifications made by tandem mass spectrometry (MS/MS) and database searching. By employing database search scores, number of tryptic termini, number of missed cleavages, and other information, the method learns to distinguish correctly from incorrectly assigned peptides in the data set and computes for each peptide assignment to an MS/MS spectrum a probability of being correct. We show that using the probabilities computed from the model, one can achieve much higher sensitivity for any given error rate compared to the results of using conventional filtering criteria. The method enables high-throughput analysis of proteomics data by eliminating the need to manually validate database search results. In addition, it can facilitate the benchmarking of various experimental procedures and serve as a common standard by which the results of different experimental groups can be compared.

ProteinProphet^TM Package

Center: Institute of System Biology

URI: PeptideProphet^TM Package

Description: Since MS/MS spectra are produced by peptides, and not proteins, there is a need for an additional statistical model for validation of the identifications at the protein level. We developed a model that has as input the list of peptides assigned to MS/MS spectra and corresponding probabilities that those peptide assignments are correct. Different peptide identifications corresponding to the same protein are combined together to estimate the probability that their corresponding protein is present in the sample. This protein grouping information is then employed to adjust the individual peptide probabilities, thus making the approach more discriminative. We also address the problem that we call degeneracy, which occurs when one peptide corresponds to several different proteins.

XPRESS

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/XPRESS.php

Description: The XPRESS software calculates the relative abundance of proteins, such as those obtained from an ICAT-reagent labeled experiment, by reconstructing the light and heavy elution profiles of the precursor ions and determining the elution areas of each peak. The software allows the specification of which residue(s) are labeled (such as cysteines for ICAT) and what the mass difference of the two isotope labels are (such as 8 Da for ICAT). There's a built in interface to the INTERACT program that allows for querying/sorting based on the expression values. Averages plus standard deviations are calculated for each protein expression value when multiple peptide measurements are available. The INTERACT interface will also display the average and median XPRESS ratio present in a dataset and correct the protein expression averages by these average and median ratio (for those cases where a systematic expression bias is present). Users are able to view the areas of integration that the software chose and adjust them as needed ... corrected expression values are then updated in the INTERACT list. For those SEQUEST users interested in using the software, ThermoFinnigan has an implementation of XPRESS in their BioWorks package.

ASAPRatio

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/ASAPRatio.php

INTERACT

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/Interact.php

Description: INTERACT was developed to address the need to curate large datasets (from tens to hundreds of LC-MS/MS runs covering multiple tens of thousands of MS/MS spectra). INTERACT allows a user to quickly interrogate such large datasets with total flexibility including filtering, sorting, grouping, and highlighting of the data. Undo-steps, restoring the full unfiltered dataset, etc. are accomplished through simple options selection and a button click. Comparisons across experiments are done using the INTERACT-Difference tool which highlights similarities and differences at either the peptide or protein levels between different experiments ... the software can handle comparisons between up to 3 experiments. The INTERACT interace is available for both SEQUEST and COMET search results.

Pep3D

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/Pep3D.php

View LC-MS and LC-MS/MS results in a 2D mz vs. time plot. If identifications are available via an INTERACT interface with PeptideProphet results, sequencing attempts and identification quality are overlayed on the plot; each spot is then a hyperlink to the ms/ms spectrum and identification. The results can be used to evaluate data quality among its many applications.

Out2Summary

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/out2summary.php

Description: Convert Sequest and TurboSequest *.out files into a single HTML-SUMMARY file ready for use with INTERACT.

CGIs

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/CGIs.php

SBEAMS

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/SBEAMS.php

Description: In order to support the data being generated by local microarray, proteomics, immunohistochemistry, and other experiments, we are developing and using SBEAMS (Systems Biology Experiment Analysis Management System), a framework for collecting, storing, and accessing data produced by a wide variety of experiments. The Systems Biology Experiment Analysis System provides a customizable framework to meet the needs of modern systems biology research. It is composed of a unified state-of-the-art relational database management system (RDBMS) back end, a collection tools to store, manage, and query experiment information and results in the RDBMS, and a web front end for accessing these tools.

Cytoscape

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/Cytoscape.php

Description: Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. The current version of Cytoscape is v2.0.

SAM: Significance Analysis of Microarrays

Center: Stanford

URI: http://www-stat.stanford.edu/%7Etibs/SAM/index.html

Description: SAM(Significance Analysis of Microarrays) is a statistical technique for finding significant genes in a set of microarray experiments. It was proposed by Tusher, Tibshirani and Chu. The software was written by Balasubramanian Narasimhan.

PAM: Prediction Analysis for Microarrays

Center: Stanford

URI: http://www-stat.stanford.edu/%7Etibs/PAM/index.html

PPC: Peak Probability Contrasts

Center: Stanford

URI: http://www-stat.stanford.edu/%7Etibs/PPC/

Nome della Proteina

Center: UT Southwest

URI: http://pathogene.swmed.edu/nome/

Description: A Protein Identification Resolution Database.

Annotated Gel Markup Language (AGML)

Center: Medical University of South Carolina

URI: http://bioinformatics.musc.edu/agml2/web/pages/schema.php

Description: Annotated Gel Markup Language, or AGML, is a language that has being proposed to markup data obtained by 2-D gel electrophorosis based on the XML language. The eXtensible Markup Language (XML) is particularly well suited to represent biological data and methods and, presently being the consensual choice in most areas. As such XML syntax notation was used to describe data acquired from 2-D gel electrophoresis and mass spectrometry. The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases. Click on the icon for the article describing AGML. Also visit other sites for additional specific information.

Minimum Information about Gel Electrophoresis Protocols (MI2DG)

Center: Medical University of South Carolina

URI: http://bioinformatics.musc.edu/mi2dg/web/pages/schema.php

Description: In order to make 2-D gel electrophoresis protocols machine readable a data structure needed to be designed and implemented. This was achived by creating an XML (eXtensible Markup Language) and RDF (Resource Description Framework) schema. This page gives information about the these schema and/or links to the pages describing them. The box on the left named 'Links' contains links to XML schema, element list and descriptions and links to MO2DG pages.

Basic Ontology for Scientific Study (BOSS)

Center: Administrative Center and Medical University of South Carolina

URI: http://www.charlestoncore.org/ont/boss.html

Description: BOSS is the acronym for Basic Ontology for Scientific Study. It is created to serve as the top ontology to describe scientific study in general terms. The scope of BOSS is very broad in the sense the vocabularies can be used to describe all kinds of scientific studies. An incurred consequence is that BOSS has a very coarse granualarity. However, this is the effect we want to achieve with BOSS. The BOSS concept can serve as a top ontology so to help align detailed application ontologies and a place holder for recording valuable information in the absence of one.

Charleston Core 2D Gel Ontology(CC2GO)

Center: Administrative Center and Medical University of South Carolina

URI: http://www.charlestoncore.org/ont/2005/08/gel.html

Description: The Charleston Core 2D Gel Ontology (CC2GO) defines concepts that can be used to drive the semantic access of a two-dimensional gel experiment. CC2GO defines the data semantics for the basic vocabularies that are used daily by web-bench scientists, such as "Gel" and "Spot". Our previous design CCGel tried to do too much with one ontology, unnecessarily making the ontological terms difficult to understand. In this version, instead of trying to accommodate different kind of gel, we made it clear what the Gel and Spot is actually is.

Ontology of Ontology (O3)

Center: Administrative Center and Medical University of South Carolina

URI: http://www.charlestoncore.org/ont/2005/08/o3.html

Description: Ontology of Ontology (O3) is created to introduce a few ontological engineer artifact that the authors think are critical to develope a robust and expressive ontological system. First, O3 partitions all ontology into ConcreteOntologies and Profiles. ConcreteOntologies are those ontology that create resources under their respective namespace. Profiles are those that does not. ConcreteOntologies are further divided into LocalOntologies and ComplexOntology. Local Ontology does not import foreign concepts whereas ComplexOntology does.

mzXML

Center: Institute of System Biology

URI: http://tools.proteomecenter.org/mzXMLschema.php

Proteomics Informatics Course at ISB

Center: Institute of System Biology

URI: http://www.proteomecenter.org/course.php

Description: The objective of this course is to instruct active proteomics researchers in the use of a suite of software tools designed for the analysis, validation, storage and interpretation of data obtained from large-scale quantitative proteomics experiments using the ICAT reagent labeling method, multi-dimensional chromatography and tandem mass spectrometry. Through daily lectures and hands-on exercises, each course participant should become proficient in the use of the tools.