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A Brief Description of Proteome Cluster. Proteome Cluster is developed and maintained by Bioproximity, LLC. Proteome Cluster is a web-based, high-performance computing solution for searching, storing, analyzing and viewing tandem mass spectrometry data. Searches are conducted on message passing interface (MPI) Beowulf compute clusters hosted on Amazon Web Services. Proteome Cluster uses numerous open-source algorithms including ProteoWizard (1), OpenMS (2), OMSSA (3), X! Tandem (4), X! The Upload page al...

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A Brief Description of Proteome Cluster. Proteome Cluster is developed and maintained by Bioproximity, LLC. Proteome Cluster is a web-based, high-performance computing solution for searching, storing, analyzing and viewing tandem mass spectrometry data. Searches are conducted on message passing interface (MPI) Beowulf compute clusters hosted on Amazon Web Services. Proteome Cluster uses numerous open-source algorithms including ProteoWizard (1), OpenMS (2), OMSSA (3), X! Tandem (4), X! The Upload page al...

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home | wiki.proteomecluster.com Reviews

https://wiki.proteomecluster.com

A Brief Description of Proteome Cluster. Proteome Cluster is developed and maintained by Bioproximity, LLC. Proteome Cluster is a web-based, high-performance computing solution for searching, storing, analyzing and viewing tandem mass spectrometry data. Searches are conducted on message passing interface (MPI) Beowulf compute clusters hosted on Amazon Web Services. Proteome Cluster uses numerous open-source algorithms including ProteoWizard (1), OpenMS (2), OMSSA (3), X! Tandem (4), X! The Upload page al...

INTERNAL PAGES

wiki.proteomecluster.com

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home

http://wiki.proteomecluster.com/history/home

August 04, 2015:. Updated home (markdown) [ bb1c549. August 04, 2015:. Updated home (markdown) [ 63cdcae. June 09, 2014:. Updated home (markdown) [ a7cb38f. February 22, 2014:. Updated home (markdown) [ 5a391d3. February 22, 2014:. Updated home (markdown) [ c080246. February 22, 2014:. Updated home (markdown) [ deeb2c8. February 22, 2014:. Updated home (markdown) [ 2992c16. February 22, 2014:. Updated home (markdown) [ 7a38072. January 17, 2013:. Updated home (markdown) [ 40480cf. January 16, 2013:.

2

runs

http://wiki.proteomecluster.com/runs

The Runs table displays the run name, the upload date, the file size, the number of tandem mass spectra in the file and the number of sequence tags in the file. The original run data file, the spectra file (in MGF format) and the sequence tags file may be downloaded using the download links,. Click the Public Runs button to list shared runs or the My Public button to list your runs and shared runs. Use the Filter field to filter the table list by run name or project name. Use the view results link. Selec...

3

projects overview

http://wiki.proteomecluster.com/projects-overview

The projects overview table. The projects overview table lists all projects in reverse chronological order. The table displays the number of runs in the project, the number of searches, the number of experiments, the number of attachments, the creation date, the owner, the users it is shared with and the date the project was last updated. Click the project ID link to be taken to the project page. Last edited by Anonymous.

4

project page

http://wiki.proteomecluster.com/project-page

A project page compiles all of the information about a set of runs to a single page. Many of the tables are the same as described elsewhere. At the top of the page is a field to invite other users to share the project. A summary and methods section are available for notes and describing experimental methods. The metrics table displays a number of metrics which may be used to evaluate samples and analytical performance. The runs table view results link. Last edited by Brian Balgley.

5

upload

http://wiki.proteomecluster.com/upload

The interface for uploading mass spectrometry data. The following file formats are supported for upload: MGF, mz5, mzML and mzXML. Options: high or low. Select high if you are uploading data generated by a high resolution instrument (FT, Orbi, TOF) in either mz5, mzML or mzXML formats. This will result in MS1 peak area data being extracted for the uploaded file. Select low for lwo resolution instruments or for MGF uploads. Options: yes or no. Options: 1 or more. Options: serial or parallel. Click to open...

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bioproximity.com

Protein Identification Service- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/gelc-ms-express.html

Talk to an Expert. Protein identification from gel spots or bands. UPLC-MS/MS by Q-Exactive Orbitrap mass spectrometry. From $100 per sample. 250 each, $200 for 8 or more, $150 for 24 or more, $100 for 48 or more. GeLC-MS/MS Protein Identification 10k. UPLC-MS/MS, up to 10,000 sequencing events, 15 cm column, 20 min gradient. Any acrylamide-based gel spot or band. Sample preparation best practices. See our Guide to Handling Protein Gels. And our Gel Staining Protocols. 20 min at 300 nL/min. Hunter if a s...

bioproximity.com

Protein Sample Preparation and Shipping- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/bioproximity-support.html

Talk to an Expert. 14153 Robert Paris Court. Domestic customers please ship using FedEx Priority Overnight. International customers, we recommend FedEx. Ship on dry ice. Animal tissue - fresh. Ship on dry ice. Animal tissue - fixed. 01 - 1 mg. Should be 95% pure. Cell culture - adherent. Ship on dry ice. Ship in lysis buffer. Cell culture - non-adherent. Ship on dry ice. Ship on dry ice. Precipitate volumes 10 mL. Ship on dry ice. Ship on dry ice. Cover with 100 uL 0.1% acetic acid. Ship on dry ice.

bioproximity.com

Proteome Cluster- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/proteome-cluster.html

Talk to an Expert. On-demand, scalable compute clusters for tandem mass spectrometry searches. Proteome Cluster is a web-based, high-performance computing solution for searching tandem mass spectrometry data. Searches are conducted on message passing interface (MPI) Beowulf compute clusters hosted on Amazon Web Services. Proteome Cluster is featured in an AWS Case Study here. Proteome Cluster currently supports four search algorithms:. Search outputs for X! Proteome Cluster is trouble-free:.

bioproximity.com

Proteomics Services & Protein ID- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/customers.html

Talk to an Expert. Protein identification and quantitation in a few hours from a few micrograms of protein by UPLC-MS/MS utilizing Orbitrap mass spectrometry. Protein identification in gel by LC-MS/MS from $100. Simple, rapid, very fast turn-around. Rapid, iterative, exhaustive sequencing of proteins and protein complexes. Ideal for use with affinity purified samples, antibodies or other biotherapeutics, and recombinant proteins. Proteomic Study of Entamoeba histolytica Trophozoites, Cysts, and Cyst-Like...

bioproximity.com

Protein Sample Preparation and Shipping- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/protein-sample-preparation.html

Talk to an Expert. 14153 Robert Paris Court. Domestic customers please ship using FedEx Priority Overnight. International customers, we recommend FedEx. Ship on dry ice. Animal tissue - fresh. Ship on dry ice. Animal tissue - fixed. 01 - 1 mg. Should be 95% pure. Cell culture - adherent. Ship on dry ice. Ship in lysis buffer. Cell culture - non-adherent. Ship on dry ice. Ship on dry ice. Precipitate volumes 10 mL. Ship on dry ice. Ship on dry ice. Cover with 100 uL 0.1% acetic acid. Ship on dry ice.

bioproximity.com

Sitemap- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/sitemap.html

Talk to an Expert. Bioproximity offers proteomic services: Protein Identification and quantitation by UPLC-MS/MS and LC-MS/MS, sequencing of proteins and protein complexes. Global proteomic profiling is an unbiased, shotgun proteomic assay utilizing ultra-high pressure liquid chromatography. Identify and quantify thousands of proteins. The GeLC-MS/MS express service enables identification of proteins in gel bands present at low to sub-nanogram quantities. Starting from $100 per sample. Bioproximity has b...

bioproximity.com

Protein Sequencing & Global Profiling FAQ- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/protein-sequencing.html

Talk to an Expert. How does shotgun proteomics sequence proteins? What is shotgun proteomics? The shotgun in shotgun proteomics refers to the process of cleaving one or more proteins. Into pieces. These pieces are called peptides. The process of cleaving, or digesting, proteins into constituent peptides is accomplished using enzymes such as trypsin. Trypsin cleaves C-terminal to arginine and lysine residues resulting in peptides with masses mostly in the range of 1,000 to 3,000 Daltons. Tandem, calculate...

bioproximity.com

Utility for Converting Mass Spectrometer File Formats- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/bioproximity-products.html

Talk to an Expert. Utility for Converting Mass Spectrometer File Formats. Is a free, simple utility for converting between common mass spectrometer file formats. The most common use of ms2mz is to convert proprietary vendor binary files (for example, Thermo RAW) to the standard MGF peak list format used for input to most proteomic search algorithms. We use ms2mz to prepare our files for upload. Download the exectuable here. Is a simple GUI overlaying msconvert. Part of the ProteoWizard. By default, outpu...

bioproximity.com

Utility for Converting Mass Spectrometer File Formats- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/utility-converting-mass-spectrometer-file-formats.html

Talk to an Expert. Utility for Converting Mass Spectrometer File Formats. Is a free, simple utility for converting between common mass spectrometer file formats. The most common use of ms2mz is to convert proprietary vendor binary files (for example, Thermo RAW) to the standard MGF peak list format used for input to most proteomic search algorithms. We use ms2mz to prepare our files for upload. Download the exectuable here. Is a simple GUI overlaying msconvert. Part of the ProteoWizard. By default, outpu...

bioproximity.com

Protein Sequencing & Global Profiling FAQ- Proteomics Company Bioproximity, LLC

http://www.bioproximity.com/shotgun-proteomics-applications.html

Talk to an Expert. How does shotgun proteomics sequence proteins? What is shotgun proteomics? The shotgun in shotgun proteomics refers to the process of cleaving one or more proteins. Into pieces. These pieces are called peptides. The process of cleaving, or digesting, proteins into constituent peptides is accomplished using enzymes such as trypsin. Trypsin cleaves C-terminal to arginine and lysine residues resulting in peptides with masses mostly in the range of 1,000 to 3,000 Daltons. Tandem, calculate...

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wiki.proteomecluster.com

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A Brief Description of Proteome Cluster. Proteome Cluster is developed and maintained by Bioproximity, LLC. Proteome Cluster is a web-based, high-performance computing solution for searching, storing, analyzing and viewing tandem mass spectrometry data. Searches are conducted on message passing interface (MPI) Beowulf compute clusters hosted on Amazon Web Services. Proteome Cluster uses numerous open-source algorithms including ProteoWizard (1), OpenMS (2), OMSSA (3), X! Tandem (4), X! The Upload page al...

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