SIPPER

SIPPER can be used to automatically detect and quantify partially labeled C13 peptides in a single dataset. It includes a GUI for manual visualization and annotation of detected LC-MS features. It also includes a Simple MS Viewer for exploring mass spectral data. Supports Thermo .Raw files, plus also mzXML, mzML, and mz5. In addition, there is a console version available for batch processing.

For algorithm details, see manuscript "Automated data extraction from in situ protein-stable isotope probing studies.", J Proteome Res. 2014 Mar 7;13(3):1200-10.
Abstract on PubMed

Requirements

Uses ThermoFisher.CommonCore.RawFileReader.dll to read Thermo .raw files.

Uses Proteowizard to read .mzML files

• Download the Windows 64-bit installer from https://proteowizard.sourceforge.io/

Analysis Steps

1. Copy the Thermo .Raw file to a local folder
2. Customize your parameter file, e.g. SipperTargetedWorkflowParameters1.xml
3. Define the search targets, e.g. Yellow_C13_070_targets.txt

• Required columns:
  • TargetID
  • EmpiricalFormula
  • ChargeState
  • Scan
• Optional columns:
  • Dataset
  • MassTagID

Note that the scan number of the target will be matched to the data in the comparison dataset using ChromNETTolerance, which is a value between 0 and 1. For example, a ChromNETTolerance of 0.025 means +/- 2.5% in Normalized Elution Time, where NET is determined by transforming the observed scan numbers to a range of 0 to 1.

4. Start SIPPER
5. Click AutoProcess
6. Define the paths to the input files

Description	Filename
Raw data file	Yellow_C13_070_23Mar10_Griffin_10-01-28.raw
Parameter file	SipperTargetedWorkflowParameters1.xml
Targets:	Yellow_C13_070_targets.txt

7. Click Go
8. Once processing is complete, click the X on the upper right of the Autoprocessor Window
9. Now click "View and Annotate"

• The program should have automatically loaded the results

Console Version

Program Sipper_Console.exe can be used on the command line to batch process files with SIPPER. This program works on both Windows and Linux, though on Linux you invoke it with Mono

Sipper_Console syntax

Sipper_Console.exe
 -I:DatasetFileOrDirectoryPath
 -P:ParameterFilePath
 -T:TargetsFilePath
 [-O:OutputDirectoryPath]
 [-ParamFile:ParamFileName.conf] [-CreateParamFile]

Use -I to specify the dataset file path

Use -P to specify the SIPPER parameter file path

Use -T to specify the targets file path

• As described above, the file must have columns TargetID, EmpiricalFormula, ChargeState, and Scan
• It can optionally have columns Dataset and MassTagID

Optionally use -O to specify the directory for saving results

• SIPPER will write results to a subdirectory named Results, below the path specified by -O
  • Filename: DatasetName_results.txt
• SIPPER will create a log ifle in a subdirectory named Logs, below the path specified by -O
  • Filename: DatasetName_log.txt
• If -O is not provided, results will be saved in subdirectories below the directory with the dataset file

The processing options can be specified in a parameter file using -ParamFile:Options.conf

• Define options using the format ArgumentName=Value
• Lines starting with # or ; will be treated as comments
• Additional arguments on the command line can supplement or override the arguments in the parameter file

Use -CreateParamFile to create an example parameter file

• By default, the example parameter file content is shown at the console
• To create a file named Options.conf, use -CreataParamFile:Options.conf

Contacts

Written by Gordon Slysz and Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: [email protected]
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics

License

SIPPER is licensed under the Apache License, Version 2.0; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/Apache-2.0

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.