Scaffold Software Supported Data Formats

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Jacob Lippincott
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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 

MSFragger (outside Scaffold):

Make sure to set up the search to produce a psm.tsv file using the output_format parameter. See instructions here.

External Document Resources

Scaffold 5 / 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.

  • MSFragger (outside of Scaffold) - PSM.TSV, PARAMS file and MGF
  • FragPipe - PSM.TSV, PARAMS file and MGF (Label-free only: no iTRAQ/TMT/SILAC)
  • 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
  • Spectrum Mill

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

  • Thermo RAW
  • Bruker D directory
  • mzML

Scaffold DDA

Scaffold DDA supports spectrum counting methods including: Total Spectrum Count,  Weighted Spectrum Count, and Exclusive Spectrum Count. Scaffold DDA also supports iTRAQ/TMT, SILAC, and precursor intensity quantitation. See matrix below for a complete listing of supported formats and quantitation types.

  • Raw data via Sage and MSFragger (Thermo raw, mzML, etc)
  • Scaffold 5 / Q+S (exported SFDB)
  • MSFragger/FragPipe (including MGF, mzML for spectra)
  • MaxQuant (2.2+)
  • Mascot
  • Proteome Discoverer (2.2+ up to 3.1)
  • PEAKS
  • ID Picker
  • Open format (mzIdentML, mzML)

See the Scaffold section for which search engines produce compatible precursor intensity data.

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 data (in the form of mzML) that msConvert can process, including Bruker and Agilent. For more information on formats supported by msConvert, please see ProteoWizard's documentation.

Scaffold DIA can also load exported search results from the following tools:

  • Spectronaut - CSV/TSV
  • DIA-NN - CSV/TSV
  • PaSER - CSV/TSV

See the user guide for which exported data are required.

Full Supported Formats Table

Scaffold 5 and Scaffold Q+S

scaffold_supported_files_1_.png

Scaffold DDA

dda3_matrix_chart_no-notes_MASTER.png

Scaffold Quant and Scaffold PTM

scaffold_quant_ptm_supported_files.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.

Legacy Software Supported Data Formats

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 LFQ Supported Data

Note, Scaffold LFQ is being phased out in favor of Scaffold Quant. 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.

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