Scaffold Software Supported Data Formats

The following document provides Scaffold Software compatible data formats.

Notes

Proteome Discoverer:

Due to how Byonic currently interfaces with Proteome Discoverer, Scaffold can only load data from Byonic run in PD 2.0 or 2.1. We have reached out to Byonic and are awaiting a resolution.

Run Proteome Discoverer with appropriate templates for either precursor intensity, isobaric tags or stable isotope labeling. Scaffold is not compatible with custom quantitation methods from PD.

Make sure the PDStudy file (from PD) or the PARAMS file (export from daemon) are in the same directory as the MSF for versions 2.X

Mascot Distiller:

If the DAT file is inaccessible from the server, it should be placed in the same directory as the XML and ROV files 

External Document Resources

Scaffold 5 and Scaffold Q+S

Scaffold and Scaffold Q+S support various spectrum counting methods including: Total Spectrum Count, Weighted Spectrum Count, emPAI and NSAF. Total Ion Current (TIC) is also calculated. The following search engines can be used for spectrum counting, or iTRAQ/TMT in Scaffold Q+S.

  • FragPipe- PSM.TSV and MGF
  • Byonic- MZID / MZID.GZ and MGF
  • Mascot Server- DAT or MZID / MZID.GZ and MGF
  • Mascot Distiller- XML / ROV / DAT
  • MaxQuant- combined directory
  • PEAKS- MZID / MZID.GZ and MGF
  • Proteome Discoverer (Mascot, Sequest, MS Amanda search nodes)- MSF and PDStudy or PARAMS
  • MS-GF+- MZID / MZID.GZ and MGF
  • PLGS- XML
  • Protein Pilot- MZID / MZID.GZ and MGF
  • Sequest- OUT / SQT / SRF and DTA/MS2
  • Spectrum Mill- results directory
  • X! Tandem- XML
  • mzIdentML- MZID / MZID.GZ and MGF

Scaffold and Scaffold Q+S can read and quantify based on precursor intensity data and provide retention time information from the following search engines.

  • FragPipe
  • Mascot Distiller
  • MaxQuant
  • Proteome Discoverer
  • Protein Pilot
  • Spectrum Mill

Finally, Scaffold Q+S can quantify using SILAC/Dimethyl precursor ion based quantitation from the following:

  • Mascot Distiller
  • MaxQuant
  • Proteome Discoverer
  • Protein Pilot
  • Spectrum Mill

Scaffold 5 introduced the ability to read raw data directly and preform spectrum counting based quantitation using MS Fragger integration from the following formats:

  • Thermo RAW
  • Bruker D directory
  • mzML

Scaffold LFQ Supported Data

Scaffold LFQ supports Total Spectrum Count and Weighted Spectrum Count quantitation. MZID / MZID.GZ and MGF files should be loaded.

  • Byonic
  • Mascot Server
  • PEAKS
  • Scaffold- MZID or SFDB export
  • ID Picker

If Scaffold data contained precursor intensities, these can be used for quantitation when loaded into Scaffold LFQ.

Scaffold PTM Supported Data

Scaffold PTM can quantify based on Total Spectrum Counts. MZID / MZID.GZ and MGF files should be loaded.

  • Mascot Server
  • PEAKS
  • Scaffold

Scaffold PTM can quantify based on iTRAQ/TMT or SILAC/Dimethyl labeling when data is exported from Scaffold Q+S in the SQML format.

Protein level normalization can be done with a ProteinQuanML file, also exported from Scaffold Q+S

Scaffold Elements Supported Data

Scaffold Elements can read low or high resolution raw LC-MS data with or without MS2 scans from the following instruments.

  • Thermo- RAW
  • Sciex- T2D / DAT / WIFF
  • Agilent- D Directory
  • Bruker- D Directory
  • Waters- RAW Directory

Scaffold DIA Supported Data

Scaffold DIA is tested with raw data from the following mass spectrometers.

  • Thermo- RAW
  • Sciex- WIFF

Since MSConvert is used to convert the raw data, Scaffold DIA should be able to load any windowed DIA that MSConvert can process, including Bruker and Agilent. For more information on formats supported by MSConvert, please see ProteoWizard's documentation.

Full Supported Formats Table

Scaffold 5 and Scaffold Q+S 5

scaffold_supported_files.png

Scaffold LFQ and Scaffold PTM

scaffold_lfq_ptm_supported_files_1_.png

Scaffold Elements and Scaffold DIA

scaffod_elements_dia.png

  1. Since MSConvert is used to convert the raw data, Scaffold DIA should be able to load any windowed DIA that MSConvert can process, including Bruker and Agilent. For more information on formats supported by MSConvert, please see ProteoWizard's documentation.
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