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   GPM Manuscript Collaborative Development Home Page

This project is an experiment to see if it is possible to collaboratively develop scientific manuscripts for publication in a manner similar to the RFC process for developing technical specifications. The manuscripts listed below as being in development can be downloaded and read by anyone. If you think you have something to add to a particular manuscript, simply contact the Organizer with your contributions and if they are considered to be helpful, they will be included in the drafts going forward. These contributions may be (but are not limited to):

  1. additional text or figures;
  2. edits to existing text;
  3. reference annotations; or
  4. suggestions for emphasis and improved exposition.

The Organizer is in charge of the process. When you make a contribution, please indicate whether you are willing to be an author, listed in the acknowledgements or simply wish to remain anonymous. It is up to the Organizer to decide whether a contribution will be accepted and how it will be incorporated into the draft manuscript going forward. Draft manuscripts can enter the process at any stage of completeness, so readers and contributors should understand that missing sections, references, figures, tables, etc. do not signify an intent to omit these things: they simply haven't been written yet.

   Draft Manuscripts in development

1. A Method to Characterize the Depth of a Shotgun Proteomics Experiment

Opening date: 2015/10/26
Proposed submission date: 2015/11/26
Current working document: depth_calculation.doc
All documents: versions and supplimentary material
Organizer: Ron Beavis, email: rbeavis@thegpm.org
Draft version: v.3 (2015/10/28)
Previous versions: | v.1 | v.2 |

This manuscript describes a method to generate distributions and parameters that can be used to quantify the concept of "depth" in a set of proteomics measurements. These measures can also be used to assist in the design of proteomics experiments by allowing researchers to objectively evaluate and predict the effects of changes to experimental protocols on the level of detection of proteins and peptides.

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