STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post‐Translational Modifications
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- Abstract
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Abstract
The identification of protein post?translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for performing fast and easy characterization of global PTM changes and differential comparison of PTMs across groups of data obtained from liquid chromatography?tandem mass spectrometry experiments. STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post?Translational Modification edition) is a program that was developed to facilitate the characterization of PTMs using spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs from complex data sets. The software facilitates multi?sample comparison by collating, scoring, and ranking PTMs, and by summarizing data visually. The freely available software (beta release) installs on a PC and processes data in protXML format obtained from files parsed through the Trans?Proteomic Pipeline. The easy?to?use interface allows examination of results at protein, peptide, and PTM levels, and the overall design offers tremendous flexibility that provides proteomics insight beyond simple assignment and counting. Curr. Protoc. Bioinform . 44:13.22.1?13.22.36. © 2013 by John Wiley & Sons, Inc.
Keywords: post?translational modifications; PTMs; proteomics; mass spectrometry; spectral counting; software; biomarkers
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Protocol 1: Setting Up Strap PTM Analysis
- Basic Protocol 2: Viewing STRAP PTM Results
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
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Figure 13.22.1 Flowchart of data from MS/MS to STRAP PTM. Raw data from a mass spectrometer (MGF files) are submitted to the Mascot search engine accessing UniProtKB FASTA and Unimod PTM databases. Search results (DTA files) are processed by the TPP (pepXML files) for input to PeptideProphet and then ProteinProphet. The TPP output (protXML files) are analyzed by STRAP PTM. View Image -
Figure 13.22.2 Example of format structure for protXML file showing a protein_group node containing a protein node with nested peptide nodes. View Image -
Figure 13.22.3 STRAP PTM Setup Page for loading sample files, accessing databases, and selecting analysis parameters (, step 3). View Image -
Figure 13.22.4 STRAP PTM Setup Page showing file input, one loaded protXML file, and active count (, step 5). View Image -
Figure 13.22.5 STRAP PTM Setup Page showing four loaded protXML files, active count, and Color Legend selection (, steps 6 and 7). View Image -
Figure 13.22.6 STRAP PTM Setup Page showing selections for Peptide Probability Type, Peptide Probability Cutoff, and Group Overlap of Proteins (, steps 8 to 10). View Image -
Figure 13.22.7 STRAP PTM Setup Page showing Unimod Database update, selections for Protein Sequence Database and PTM Score, and analysis start (, steps 11 to 13 and 15). View Image -
Figure 13.22.8 STRAP PTM Results Page for viewing results in tables and maps at protein, peptide, and PTM levels. An entry in the Protein Summary table is selected to populate the page after analysis (, step 1). View Image -
Figure 13.22.9 STRAP PTM Results Page showing Protein Summary table with protein CD40L_HUMAN‐2 selected (, step 2). View Image -
Figure 13.22.10 STRAP PTM Results Page showing Global PTMs table. Unique PTMs are listed for all proteins in the Protein Summary table (, step 3). View Image -
Figure 13.22.11 STRAP PTM Results Page showing PTM Map for protein CD40L_HUMAN‐2. Tab for PTM Map is clicked (, step 4). View Image -
Figure 13.22.12 STRAP PTM Results Page showing close‐up of PTM Map for protein CD40L_HUMAN‐2 in all groups. Locations of PTMs are indicated by colored bars in the protein sequence and by colored bars in the protein bar model. Details of modified cysteine (C88) are shown in the box (, step 4). View Image -
Figure 13.22.13 STRAP PTM Results Page showing close‐up of PTM Map for protein CD40L_HUMAN‐2 in group C1. Locations of PTMs are indicated by red bars in the protein sequence and by red bars in the protein bar model (, step 4). View Image -
Figure 13.22.14 STRAP PTM Results Page showing Peptide Summary table with peptide EASSQAPFIASLCLK selected. Tab for Peptide Information is clicked (, steps 5 to 6). View Image -
Figure 13.22.15 STRAP PTM Results Page showing Peptide Summary Statistics table for protein CD40L_HUMAN‐2. Tab for Peptide Information is clicked (, step 7). View Image -
Figure 13.22.16 STRAP PTM Results Page showing Peptide PTM Summary table for peptide EASSQAPFIASLCLK. Specific PTMs and specific sites are listed, together with PTM score and scoring factors. PTM hyperlink to Unimod Web site is indicated. Tabs for Peptide Information and Peptide PTM Summary are clicked (, step 8). View Image -
Figure 13.22.17 STRAP PTM Results Page showing Peptide PTM Details table for peptide EASSQAPFIASLCLK. All entries are listed by group with PTM and probability information. Each entry shows the sequence with PTM locations and details. Tabs for Peptide Information and Peptide PTM Details are clicked (, step 9). View Image -
Figure 13.22.18 STRAP PTM Results Page showing Summary of PTMs on Protein table for protein CD40L_HUMAN‐2. Tab for PTM Overview is clicked (, step 10). View Image -
Figure 13.22.19 STRAP PTM Results Page showing close‐up of Summary of PTMs on Protein table for protein CD40L_HUMAN‐2. Entries are sorted by decreasing Modification Mass with results for residues C88, Y39, and Y40 highlighted (, steps 11 to 14). View Image
Videos
Literature Cited
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