DIA-Umpire:

Computational analysis for mass spectrometry-based proteomics data

The followings are the brief descriptions for each NetBeans project

DIA_Umpire_SE

The first step of DIA-Umpire analysis. It is a signal extraction module to generate pseudo MS/MS spectra given a DIA file

• java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire.se_params

DIA_Umpire_LCMSIDGen

After untargeted identification analysis, DIA-Umpire generates untargeted peptide IDs using pepXML files and output as *LCMSID file, which is the input file format for internal and external library searches.

• java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire.module_params

DIA_Umpire_IntLibSearch

DIA-Umpire internal library search that uses *LCMSID file as input file. The input *LCMSID file will be updated after the process.

• java -jar -Xmx10G DIA_Umpire_IntLibSearch.jar diaumpire.module_params

DIA_Umpire_ExtLibSearch

DIA-Umpire external library search that uses *LCMSID file and a spectral library as input files. The input *LCMSID file will be updated after the process.

• java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire.module_params

DIA_Umpire_ProtQuant

DIA-Umpire protein quantification module takes *LCMSID file as input, the output is protein, peptide, fragment quantification results in csv format

• java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire.module_params

DIA-Umpire_To_Skyline

Module to generate raw-intensity pseudo MS/MS spectra. (without intensity adjustments)

DIA-Umpire

Main DIA-Umpire class libraries

• ExternalPackages: external packages, currently including JAligner, SortedListLib, JMEF, and a traML parser developed by ISB.

• FDREstimator: wrapper to generate FDR filtered protein and peptide lists

• MSUmpire: Umpire libraries

  • BaseDataStructure : basic data structure, including x-y pair value data, scan data, and parameter setting class etc.
  • DIA : DIA specific classes
  • FragmentLib : Fragment library manager, basically it's a spectral library
  • LCMSPeakStructure : Data structure classes for MS1 or MS2 peak for to a LCMS run
  • MathPackage : Math calculation classes
  • PSMDataStructure : Data structure classes related to Mass-spec based identifications, ranging from PSM, peptide ion, protein and identification data structure for a LC-MS run (LCMSID.java). In addition, this package includes processing manager to extract PTM and peptide fragment information generated from Compomics library.
  • PeakDataStructure : Data structure classes related to peak data, from peak curve, peak isotope cluster, and peak smoothing algorithms.
  • PeptidePeakClusterDetection : Processing classes to detect peak features
  • SearchResultParser : PepXML, ProtXML parsers
  • SeqUtility : Classes for sequence processing, including FastaParser and shuffled sequence generator
  • SpectralProcessingModule : Spectrum peak processing classes
  • SpectrumParser: mzXML, mzML parsers
  • Utility: Other classes

• resource: all resource files in text format

MS1Quant

DDA-based MS1 quantification tool based on the feature detection algorithm.