This topic provides information about the templates for top-down analysis.

The following table lists the analysis and workflow templates for study creation.

Table Analysis Templates, Processing Workflow Templates, and Consensus Workflow Templates

Template Name

Description

Analysis Templates

Includes both processing workflow and consensus workflow.

PSPD 1 percent FDR LFQ for HI HI data.PDANALYSIS

Includes the discovery proteomics search nodes and the nodes required to perform label-free proteoform quantitation on high resolution data.

PSPD 1 percent FDR LFQ for Med HI data.PDANALYSIS

Includes the nodes for discovery proteomics searches and label-free proteoform quantitation on medium high resolution data.

PSPD FASTA Exporter.PDANALYSIS (analysis template)

Enables export of FASTA files from Proteome Discoverer for subsequent ProSight database creation in the ProSightPD Database Manager. Enables you to utilize the FASTA database utilities in PD and export FASTA files not formated in UniProt format.

PSPD PTCR tMS2 Discovery Proteomics with FDR.PDANALYSIS

Supports PTCR data collected as a pseudo MS1. In this method PTCR is used on a small window of the m/z spectrum. The resulting MS2 scan, which is the PTCR scan, is treated as the precursor containing scan. The subsequent MS3 scan is the fragmentation of the PTCR window used to make PrSMs. This workflow uses a special cRAWler node to analyze discovery PTCR data.

PSPD Hi Hi TopDownStandard.PDANALYSIS Analysis Template

Designed to be used with the provided Pierce TopDown Standard database and RAW file.

PSPD Med HI.PDANALYSIS Analysis Template

Built for data with isotopically unresolved precursors. Covers the largest proteoform space including all annotated forms (PTMs, SNPs, and so on) in your database (annotated proteoform search), unknown truncations (subsequence search) and unknown modifications through the wide mass (1000 Da) tolerance annotated proteoform search. This search is the most time consuming. Designed for traditional high throughput LC/MS based workflows. Results are filtered to 1% FDR.

PSPD Discovery Proteomics with FDR.PDANALYSIS

Identifies all proteoforms found in the user’s database, including known modifications. This search does not find unknown truncated proteoforms.

This template is designed for quick analysis of traditional high throughput LC/MS based workflows. Results are filtered to 1% FDR.

PSPD Comprehensive Discovery Proteomics with FDR.PDANALYSIS

Covers the largest proteoform space including all annotated forms (PTMs, SNPs, and so on) in your database (annotated proteoform search), unknown truncations (subsequence search), and unknown modifications through the wide mass (1000 Da) tolerance annotated proteoform search. This search is the most time consuming.

Designed for traditional high throughput LC/MS based workflows. Results are filtered to 1% FDR.

PSPD Med HI Analysis Template.PDANALYSIS

Intended for data with non-isotopically resolved precursors.

Typically, this search template is used for lower resolution precursor scans or when analyzing larger or highly charged proteoforms. Results are filtered to 1% FDR.

PSPD Truncation Subsequence Search with FDR.PDANALYSIS

Searches for truncated sequences, including those with any known PTMs or modifications.

PSPD Single Proteoform.PDANALYSIS

Searches for a single user-defined proteoform, which does not require a database. This workflow is suitable for identifying one species in a complex LC/MS experiment or to confirm the identify of a single species from a mixture of infused proteoforms.

Processing Workflow Templates

 

PSPD MS2 Precursor with MS3 Fragmentation HI HI.pdProcessingWF

Supports analysis of “complex-down” data. The initial fragmentation event generates monomers, which are targeted for MS3 fragmentation. The sequence information is derived from the MS3 data (PrSMs come from MS3) This template supports isotopically resolved species (monomer isotopes are resolved).

PSPD Comprehensive Discovery Proteomics with FDR for Unresolved Precursors.pdProcessingWF

ProSightPD processing workflow for unresolved precursor spectra. This workflow includes: Narrow Tolerance Annotated Proteoform Search, Wide Tolerance Annotated Proteoform Search, and Subsequence searches. These searches combined create a comprehensive search strategy.

PSPD PTCR Discovery Proteomics with FDR.pdProcessingWF

Identifies larger proteoforms from PTCR data.

PSPD Discovery Proteomics with FDR for HI HI data.pdProcessingWF

Performs searches for high-resolution data.

PSPD Discovery Proteomics with FDR for Unresolved Med HI data.pdProcessingWF

Performs proteoform identification on data containing unresolved precursors. Must be used with FDR nodes in consensus workflow.

PSPD LFQ for HI HI data.pdProcessingWF

Performs searches for high resolution data with LFQ analysis. Must be used with LFQ nodes in consensus workflow for LFQ results.

PSPD LFQ for Med HI data.pdProcessingWF

Performs searches for medium high data with LFQ analysis. For label-free results, use with LFQ nodes in the consensus workflow.

PSPD Comprehensive Discovery Proteomics with FDR for HI HI data.pdProcessingWF

Performs both annotated and subsequence searches for high resolution data (resolved precursors). This parameter must be used with FDR nodes in consensus workflow.

PSPD Single Proteoform Search.pdProcessingWF

Performs single user-defined proteoform searches.

PSPD Truncation Search with FDR.pdProcessingWF

Performs subsequence search only for high resolution data. Must be used with FDR nodes in consensus workflow.

Consensus Workflow Templates

 

PSPD 1 percent FDR Consensus.pdConsensusWF

Returns results filtered to 1% FDR.

PSPD 1 percent FDR LFQ for HI HI with PFR Annotation data.pdConsensusWF

Returns results filtered to 1% FDR includes PFR annotation.

PSPD 1 percent FDR LFQ for HI HI data.pdConsensusWF

Returns LFQ data with 1% FDR.

PSPD No FDR Consensus.pdConsensusWF

Returns results without FDR control.

PSPD 1 percent FDR LFQ for Unresolved Precursors data.pdConsensusWF

Returns Med/Hi LFQ data with 1% FDR.