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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Protein Prospector Resource Report Resource Website 500+ mentions |
Protein Prospector (RRID:SCR_014558) | software resource, software toolkit | A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass. | database search program, database search, database management, peptide, protein, mass spectrometry, ms, utility program, batch msms, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
Open source, Freely available to academic researchers | biotools:proteinprospector | https://bio.tools/proteinprospector | SCR_014558 | ProteinProspector | 2026-09-05 06:32:58 | 595 | |||||||
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GPS Resource Report Resource Website 50+ mentions |
GPS (RRID:SCR_016374) | GPS | algorithm resource, software resource | Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode. | phosphorylate, protein, seq, predictive, substrate, site, kinase, mass spectrometry | PMID:18463090 | Free for academic use, Request for commercial use, Available for download | SCR_016374 | Group-based Prediction System, GPS: Group-based Prediction System, Group-based Prediction System (GPS) | 2026-09-05 06:33:01 | 69 | ||||||||
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kbDNA Inc. Resource Report Resource Website |
kbDNA Inc. (RRID:SCR_016570) | biomaterial supply resource, material resource | Commercial provider of antibodies, antigens and recombinant proteins from Braintree, Massachusetts . Biotechnology company which provides custom oligonucleotides synthesis service. | commercial, biotechnology, company, antibody, antigen, recombinant, protein, custom, synthesis, oligonucleotide | SCR_016570 | 2026-09-05 06:33:02 | 0 | ||||||||||||
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NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis Resource Report Resource Website 1+ mentions |
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) | Mass Spectrometry Resource, WU Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry | systems biology technology center, mass spectrometry, protein, lipid, metaboilite, biomarker, isotope, analysis | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIGMS ; NCRR 2P41RR00954 |
nlx_152688 | SCR_009009 | Mass Spectrometry Resource at Washington University in St. Louis, Washington University Mass Spectrometry Resource | 2026-09-05 06:33:30 | 1 | |||||||
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Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center Resource Report Resource Website |
Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) | BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics. | RT PCR, transcriptome, epigenome, metabolomics, profiling, assay, protein, expression, pathway, data, bioinformatics, analysis, next, generation, sequencing, human, mouse, array, tissue, imaging |
is listed by: Eagle I is related to: Beth Israel Deaconess Medical Center Labs and Facilities is related to: Harvard University Labs and Facilities has parent organization: Harvard University; Cambridge; Massachusetts |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156126 | http://www.bidmcgenomics.org/ | SCR_009668 | Beth Israel Deaconess Medical Center, BIDMC | 2026-09-05 06:33:30 | 0 | ||||||
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Salk Institute Peptide Synthesis Core Facility Resource Report Resource Website 1+ mentions |
Salk Institute Peptide Synthesis Core Facility (RRID:SCR_014848) | access service resource, core facility, service resource | Core facility that provides services such as peptide synthesis, incorporation of non-conventional and/or modified amino acids, HPCL characterization and purification, and Mass spec analysis. | core facility, la jolla, peptide synthesis, protein, amino acid, hpcl, mass spec | Salk Institute Peptide Synthesis Core Facility ; NCI CCSG P30 014195 |
Commercially available | SCR_014848 | 2026-09-05 06:34:00 | 1 | ||||||||||
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Sanford Burnham Prebys Medical Discovery Institute NMR Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute NMR Facility (RRID:SCR_014861) | instrument supplier, material resource | Facility that acts as a centralized shared resource for NMR studies on proteins, peptides, small molecules, and carbohydrates in solution or in solid state. It provides instrumentation and expertise for NMR data collection. It also provides consultation with investigators on the feasibility of NMR for structural studies of protein candidates, as well as the optimal method to obtain solution structures and binding information by multi-dimensional NMR techniques. It can also train users in basic spectrometer operations, trouble-shoot for instrumental and operational problems, and set up NMR experiments for users as requested. | facility, medical, nmr, protein, peptide, small molecules, carbohydrates, data collection, consultation, spectrometer, linux, software, analysis | Commercially available | SCR_014861 | SBP NMR Facility, SBP Medical Discovery Institute NMR Facility | 2026-09-05 06:34:00 | 0 | ||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core (RRID:SCR_014862) | instrument supplier, material resource | Facility that provides a variety of analytical services focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. Examples of services include quality control of protein samples (folding, stability, aggregation); measuring molecular weight of proteins, protein complexes, oligomers and assemblies; charcaterizing protein conformation and shape in solution; determining oligomeric state of protein (including stoichiometry and Kd for self-association) and measuring protein binding to proteins, peptides, small molecules, compounds, metals, nucleotides and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy). | facility, la jolla, protein, analysis, quality control, molecular weight, stoichiometry | Commercially available | SCR_014862 | SBP Medical Discovery Institute Protein Analysis Core, SBP Protein Analysis Core | 2026-09-05 06:34:00 | 0 | ||||||||||
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MIT KIICR Biopolymers and Proteomics Core Facility Resource Report Resource Website 1+ mentions |
MIT KIICR Biopolymers and Proteomics Core Facility (RRID:SCR_017737) | access service resource, core facility, service resource | Facility provides integrated synthetic and analytical capabilities for biological materials, including proteins, peptides, and nanoparticles, range of technical expertise and instrumentation. Access is available to all members of MIT community. Priority access is given to KI members, NCI-funded research projects and other contributing user groups in recognition of funding support. In special circumstances, access may be available to non-MIT users. | Synthetic, analytical, bioplymer, protein, peptide, nanoparticles, technical, expertise, instrumentation, MIT, service, core | National Cancer Institute Cancer Center Support Grant | Restricted | ABRF_213 | SCR_017737 | KI Swanson Biotechnology Center Biopolymers and Proteomics Core Facility | 2026-09-05 06:34:11 | 1 | ||||||||
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Zurich University Functional Genomics Center Core Facility Resource Report Resource Website |
Zurich University Functional Genomics Center Core Facility (RRID:SCR_017742) | FGCZ | access service resource, core facility, service resource | Laboratory performs services in proteomics, genomics and metabolomics by FGCZ personnel without need for user to access labs. Services include Proteomics:Protein identification,quantification,characterization,Glycan/glycoprotein analyses, Analysis of Biomolecules, Fractionation; Genomics:DNA sequencing, RNA sequencing; Metabolomics/Biophysics services. | Proteomics, genomics, metabolomics, protein, identification, quantification, characterization, glycan, glycoprotein, ananlysis, biomolecule, fractionation, genomics, DNA, RNA, sequencing, metabolomics, biophysics, service, core | ABRF_204 | SCR_017742 | Functional Genomics Center Zurich | 2026-09-05 06:34:11 | 0 | |||||||||
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Rhode Island INBRE Molecular Informatics Core Facility Resource Report Resource Website 10+ mentions |
Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) | access service resource, core facility, service resource | Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research. | Analysis, interpretation, nucleotide, amino acid, sequence, protein, domain, structure, service, 3D visualization, modeling, USEDit |
has parent organization: University of Rhode Island; Rhode Island; USA has parent organization: USEDit |
NIGMS P20 GM103430 | Open | ABRF_3 | SCR_017685 | Rhode Island INBRE Molecular Informatics, RI-INBRE Bioinformatics Core; RI Genomics and Sequencing Center | 2026-09-05 06:34:10 | 16 | |||||||
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University of Texas MD Anderson Cancer Center Proteomics Core Facility Resource Report Resource Website |
University of Texas MD Anderson Cancer Center Proteomics Core Facility (RRID:SCR_017731) | access service resource, core facility, service resource | Facility provides mass spectrometry analysis of proteins. Provides access to mass spectrometry based proteomics technologies and services including Protein Identification, Molecular Weight Determination, Quantitative Protein Analysis, Post-translational Modification Analysis, LC or LC-MS Analysis, Equipment Usage, Additional Data Analysis:Bioinformatics, statistics, pathway analysis and Assistance preparing materials for manuscripts or grants.Consultations for custom assays for other MS Services are also available. | Mass, spectrometry, analysis, protein, proteomics, service | NCI P30 CA016672; NIH Office of the Director S10 OD012304 |
Open | ABRF_186 | SCR_017731 | Proteomics Facility | 2026-09-05 06:34:11 | 0 | ||||||||
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Maine Medical Center Research Institute Proteomics and Lipidomics Analysis Core Facility Resource Report Resource Website |
Maine Medical Center Research Institute Proteomics and Lipidomics Analysis Core Facility (RRID:SCR_017730) | access service resource, core facility, service resource | Core provides protein and small molecule structural and functional analysis, and quantitation using technologies and software applications. Services in Nano-liquid chromatography,Protein identification and quantitation using SWATH,Protein post translational modification identification,Lipid profiling and identification (MS/MSALL),Targeted multiple reaction monitoring (MRM) for lipids. | Protein, small, molecule, structural, functional, analysis, quantitation, nano, liquid, chromatography, lipid, SWATH | Vascular Biology Center of Biomedical Research Excellence (COBRE) Program | Restricted | ABRF_170 | SCR_017730 | MMRC Proteomics and Lipidomics Analysis | 2026-09-05 06:34:11 | 0 | ||||||||
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Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility Resource Report Resource Website |
Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility (RRID:SCR_017695) | REPR | access service resource, core facility, service resource | Resource offers range of mass spectrometry instrumentation, expertise in analysis of RNA, RNA modifications, and proteins involved in RNA metabolism/regulation, supports projects involving analysis of biomolecules, metabolites, and small synthetic molecules, provides consulting on experimental design, sample preparation and data interpretation, whole project development and grant writing contributions. | Mass, spectrometry, instrument, analysis, RNA, protein, biomolecule, data, grant, project, service, core | Open | ABRF_113, SCR_017715 | SCR_017695 | RNA Epitranscriptomics and Proteomics Resources | 2026-09-05 06:34:10 | 0 | ||||||||
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University of Nevada at Reno Nevada Proteomics Center Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada at Reno Nevada Proteomics Center Core Facility (RRID:SCR_017761) | access service resource, core facility, service resource | Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling. | Mass, spectral, proteomic, analysis, qualitative, quantitative, protein, plasma, serum, tissue, cell, line, physiological, pathway, interaction, signaling, stury, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20 GM103440 | Open | SCR_011043, SciEx_9701, ABRF_281 | https://coremarketplace.org/?FacilityID=281&citation=1 | SCR_017761 | Mick Hitchcock, Ph.D. Nevada Proteomics Center | 2026-09-05 06:34:11 | 6 | ||||||
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Virginia Commonwealth University Chemical and Proteomic Mass Spectrometry Core Facility Resource Report Resource Website |
Virginia Commonwealth University Chemical and Proteomic Mass Spectrometry Core Facility (RRID:SCR_017806) | CPMSC | access service resource, core facility, service resource | Core provides mass spectrometric services, from basic mass measurement to complex proteome analyses.Services include basic mass measurement, ESI-MS/MS,LC-MS,Exact mass measurement,Protein identification. | Mass, spectrometry, measurement, proteome, analysis, protein, identification, service, core | Open | ABRF_515 | SCR_017806 | Chemical and Proteomic Mass Spectrometry Core Facility | 2026-09-05 06:34:13 | 0 | ||||||||
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Texas University Health Science Center at San Antonio Biomolecular NMR Core Facility Resource Report Resource Website |
Texas University Health Science Center at San Antonio Biomolecular NMR Core Facility (RRID:SCR_017775) | access service resource, core facility, service resource | Core offers high field NMR instrumentation for structural studies of biological macromolecules. Instrumentation includes four-channel Bruker Avance 500, 600, and 700 MHz NMR spectrometers, ultra high sensitivity 5mm 1H-13C-15N triple-resonance cold probe for 600 MHz spectrometers. Service include acquisition and analysis of required spectra for elucidation of small molecule structures (includes synthetic molecules, natural products, cofactors, lipids, and short peptides (30 amino acids or less)). Types of projects conducted collaboratively include determination of three-dimensional structures of biological macromolecules, including proteins and nucleic acids, both alone and as complexes with various ligands. | Biomolecular, NMR, structural, study, macromolecule, spectrometry, acquisition, analysis, spectra, small, molecule, structure, lipid, peptide, cofactor, protein, nucleic acid, ligand, service, core | Houston Endowment ; NIH National Center for Research Resources ; U. Texas Permanant University Fund ; User Fees ; UT Health San Antonio Children Cancer Research Center ; UT Health San Antonio Core Facilities Committee ; UT Health San Antonio MD Anderson Cancer Center |
ABRF_353 | SCR_017775 | Biomolecular NMR Core | 2026-09-05 06:34:12 | 0 | |||||||||
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Saint Louis University School of Medicine Protein Core Facility Resource Report Resource Website |
Saint Louis University School of Medicine Protein Core Facility (RRID:SCR_017811) | access service resource, core facility, service resource | Core facility that supports expression, purification, and analysis of reagent and preclinical proteins by providing instrumentation and consultation for protein production from small to large scale. Available equipment includes shaking incubators, 5 L fermentor, high pressure cell disruptor, hollow fiber concentrator, Maxwell16 magnetic bead purification system, AKTA Purifier chromatograph, analytical ultracentrifuge, analytical HPLC, and MALDI-QIT-TOF mass spectrometer. | Protein, expression, purification, analysis, reagent, preclinical, production, HPLC, mass, spectrometer, service, core | Open | ABRF_564 | SCR_017811 | Protein Core Facility | 2026-09-05 06:34:13 | 0 | |||||||||
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Kansas University at Lawrence Protein Production Group Core Facility Resource Report Resource Website |
Kansas University at Lawrence Protein Production Group Core Facility (RRID:SCR_017749) | PPG | access service resource, core facility, service resource | Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies. | Protein, production, purification, expression, cloning, service, core | NCRR P20 RR017708; NIGMS P20 GM103420; NIGMS P30 GM110761 |
Open | ABRF_249 | SCR_017749 | KU COBRE Protein Production Group | 2026-09-05 06:34:11 | 0 | |||||||
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Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility Resource Report Resource Website |
Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility (RRID:SCR_017751) | ABL | access service resource, core facility, service resource | Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation. | Data, analysis, mining, pathway, network, interaction, prediction, protein, structure, function, stability, sequence, domain, acquisition, management, report, grant, manuscript, service, core | Open | ABRF_252 | SCR_017751 | Molecular Graphics and Modeling Laboratory | 2026-09-05 06:34:11 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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