MIAPE: Module TemplateVersion 1.0, 5th December, 2005.

Using this documentThis document lays out the look and feel of, and the content required for a MIAPE module. All of the text is annotated using the Microsoft Word commenting system (as in ‘Track Changes’), which works well with later version of the Microsoft Office tool Suite. Authors should attempt to use the same fonts and layout as in this document, to maintain consistent L&F between modules and the parent document.

‘Literal text’ should be kept as presented in this document, although runs of literal text may contain items to be replaced or deleted as necessary.

‘Guidance text’ is provided to describe the content of a particular paragraph or section, and should be replaced in the final document with the text so described.

‘Replace with…’ instructions should be adhered to as described.

‘Optional text’ should be deleted as necessary.

‘Other instructions in comments’ should be adhered to as described.

Chris Taylor (chris.taylor@ebi.ac.uk), 2005-12-05.

MIAPE: [Brief Catchy Title]Version 1.0, 5th December, 2005.

This module identifies the minimum information required to report [the use of] [technique(s)] in a proteomics experiment, in a manner compliant with the aims as laid out in the ‘MIAPE Principles’ document (latest version available from http://psidev.sf.net/gps/miape/).

Introduction

This opening paragraph very briefly {<=100 words} introduces the general area to which this module has applicability (essentially an expansion of the title); and should finish by describing the manner of application of the general ‘MIAPE Principles’ in this particular instance. For a full discussion of the principles underlying this specification, please refer to the MIAPE ‘Principles’ document, which can be found on the MIAPE website†.

The next section {<=200 words} more specifically demarcates the scope of this module. First, provide a terse list of major features. Next, a similarly terse list of things not included (both to more clearly mark the boundary and to list exceptions that might otherwise have been assumed to fall within scope). Terminate this section with the following statement: Items falling outside the scope of this module may be captured in complementary modules, which can be obtained from the website†. Note that subsequent versions of this document may have altered scope, as will almost certainly be the case for all the MIAPE modules.

The following section, detailing the reporting requirements for [the use of][technique(s)], is subdivided as follows:1. Supply a numbered list of the

subsections into which the specific reporting requirements specification is subdivided. Try to keep eachlist item brief, but be sure to describe the content fully enough to be used as an informal index.

2. [item]

Reporting requirement for[technique(s)]

1. Major Heading (e.g. General Features)

a) Subheading– Item– Item

b) Subheading– Item– Item

2. Second Major Heading

† http://psidev.sf.net/gps/miape/

Advisory notes can be inserted into this area after each major heading as appropriate. These notes can refer to other sections by their head/subhead, i.e. (2a).a) Subheading

– Items requiring no action (e.g. exceptions) can be listed as normal items, but should be italicised. Items can also refer to other sections by their head/subhead, i.e. (2a).

– Item– etc.

Summary

The MIAPE: [Brief Catchy Title] minimum reporting requirements for [the use of][technique(s)] specify that a significant degree of detail be captured, for [terse list of areas of applicability]. However, it is clear that providing the information required by this document will enable the effective interpretation and assessment of [data/metadata from this area] and potentially, support experimental corroboration. Much of the information required herein may already be stored in an electronic format, or exportable from the instrument; we anticipate further automation of this process.

These guidelines will evolve. To contribute, or to track the process to remain ‘MIAPE-compliant’, browse to the website at http://psidev.sf.net/gps/miape

Appendix One. The MIAPE: [Brief Catchy Title] glossary of required items

Classification Definition

1. Major Heading — (a) Subheading

Item Full definition, formatting requirements and ideally a brief example (N.B. dates should always be required as YYYY-MM-DD).

Item Full definition, formatting requirements and ideally a brief example.1. Major Heading — (b) Subheading

Item Full definition, formatting requirements and ideally a brief example.Item Full definition, formatting requirements and ideally a brief example.

2. Second Major Heading — any notes pertaining to this whole section should be entered here, in italics, followed by the normal section header

2. Second Major Heading — (a) SubheadingItalicised item requiring little/no action These should still be entered and described as normal in this appendix.Item Full definition, formatting requirements and ideally a brief example.etc. Full definition, formatting requirements and ideally a brief example.