Organizing MSMS Proteomic Data for Publication with Scaffold

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Organizing MS/MS Proteomic Data for Publication
with Scaffold

• Brian C. Searle
• Proteome Software Inc.
• Portland, Oregon
• ABRF2009, Memphis TN
• February 10th, 2009

Creative Commons Attribution
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Publication Standards

• In 2006 MCP published guidelines for reporting
  peptide and protein identifications
• Other proteomics journals have adopted similar
  standards

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What do the Guidelines Do?

• The guidelines ensure enough information to
• Understand and critically assess the results
• Enforce a low level of reliability
• Provide enough data concerning potentially
  questionable results to allow for reassessment

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What do the Guidelines Do?

• The guidelines ensure enough information to
• Understand and critically assess the results
• Enforce a low level of reliability
• Provide enough data concerning potentially
  questionable results to allow for reassessment
• Publication guidelines have played a critical
  role in the acceptance of proteomic analysis

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Publication Standards are Hard!
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Publication Standards are Hard!

• They're hard for
• the authors who have to comply

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Publication Standards are Hard!

• They're hard for
• the authors who have to comply
• the reviewers who must police compliance

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Publication Standards are Hard!

• They're hard for
• the authors who have to comply
• the reviewers who must police compliance
• the journals because theres a huge amount of
  supplemental data in non-standard formats
• PowerPoint guarantee readability, but difficult
  to use
• RAW file formats can expire, but are much more
  useful

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Publication Standards are Hard!

• They're hard for
• the authors who have to comply
• the reviewers who must police compliance
• the journals because theres a huge amount of
  supplemental data in non-standard formats
• But they dont have to be!

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Scaffold Goals

• Make it easier to organize data
• Make tables useful for publication
• Make figures that could be dropped directly into
  manuscripts
• Clear fit when the guidelines were announced

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Scaffold Makes theGuidelines Easier for Authors

• Collate relevant data from search engine files
• Most search engines supported Mascot, SEQUEST,
  X! Tandem, Phenyx, SpectrumMill, OMSSA, IdentityE

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Scaffold Makes theGuidelines Easier for Authors

• Collate relevant data from search engine files
• Most search engines supported Mascot, SEQUEST,
  X! Tandem, Phenyx, SpectrumMill, OMSSA, IdentityE
• Collapse related parameters across all files
• Clearly point out missing metadata
• Produce comparable search engine and instrument
  independent probabilities

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Collate Relevant Data

• Peak picking software, version, altered
  parameters
• Database Selection
• Database name and version
• Species restriction
• Number of proteins searched
• Database search parameters
• Search engine name and version
• Enzyme specificity
• missed cleavages
• Fixed/variable modifications
• Mass tolerances
• Peptide selection criteria

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Collate Relevant Data

• Peak picking software, version, altered
  parameters
• Database Selection
• Database name and version
• Species restriction
• Number of proteins searched
• Database search parameters
• Search engine name and version
• Enzyme specificity
• missed cleavages
• Fixed/variable modifications
• Mass tolerances
• Peptide selection criteria

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Collate Relevant Data
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Collate Relevant Data

• This Button Gets
• Protein accession numbers
• Number of unique peptides
• sequence coverage

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Collate Relevant Data

• While This Button Gets
• Peptide sequences identified
• Precursor m/z and charge
• Score and peptide probability

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Collate Relevant Data

• One hit wonders and modifications require
  validation
• Distribute the Scaffold file to reviewers

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Collate Relevant Data

• Similar table and reports for iTRAQ and TMT
  quantitative data in Scaffold Q
• Thats it!

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Making the Guidelines Easier for Reviewers to
Police

• All metadata is guaranteed to be present

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Making the Guidelines Easier for Reviewers to
Police

• All metadata is guaranteed to be present
• Quick to review key proteins and spectra

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Making the Guidelines Easier for Reviewers to
Police

• All metadata is guaranteed to be present
• Quick to review key proteins and spectra
• Easy to validate statistical assumptions

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Probability Assumptions Usually Work
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But Not Always!
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Distributing Guideline Compliant Data

• Journals can distribute Scaffold files containing
  the entire data set

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Distributing Guideline Compliant Data

• Journals can distribute Scaffold files containing
  the entire data set
• Authors can share their raw data
• Peak list exports for a variety of formats
• (MGF, DTA, PKL, etc)

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Distributing Guideline Compliant Data

• Journals can distribute Scaffold files containing
  the entire data set
• Authors can share their raw data
• Peak list exports for a variety of formats
• (MGF, DTA, PKL, etc)
• Journals are allowed to distribute the original
  version of the free viewer so the files can
  ALWAYS be opened!

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Conclusions

• Scaffold makes it
• Easier to pass publishing data guidelines
• Easier to review data and to police standards
• Easier to safely distribute supplemental material
  in a useful format