Computational Mass Spectrometry @ Pacific Northwest National Laboratory

Richland, WA

Pinned Repositories

AutoCCS
Automated Collision Cross Section calculation software for ion mobility spectrometry-mass spectrometry
Language:Python8 5 11
DB-Schema-Export-Tool
Exports SQL Server and Postgres database objects as schema files. Exported objects include tables, views, stored procedures, and functions, plus also database properties including database roles and logins. The program can also export table data to create SQL files with an Insert Into statement for each row.
Language:C#12 6 27
DeconTools
Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
Language:C#17 21 74
Informed-Proteomics
Top down / bottom up, MS/MS analysis tool for DDA and DIA mass spectrometry data
Language:C#29 33 339
LIQUID
Software tool for identifying lipids in LC-MS/MS-based lipidomics data
Language:C#19 10 52
MASIC
MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis, characterizing the peak(s) in each SIC, computing peak statistics including elution time of the peak apex, peak area, and peak signal/noise. It can also extract reporter ion abundances (e.g. iTRAQ or TMT).
Language:C#15 6 54
Molecular-Weight-Calculator-DLL
The Molecular Weight Calculator can be used to calculate the molecular weight and percent composition of chemical formulas and amino acids (peptides). It includes several other utility modules and is available as both a GUI version and a C# DLL version.
Language:C#10 22 03
Molecular-Weight-Calculator-VB6
Molecular Weight Calculator (MWTWin): Graphical program written in VB6 with numerous mass calculation utilities.
Language:VBA10 8 36
MS-File-Info-Scanner
Examines a series of MS data files (or data directories) and extracts the acquisition start and end times, number of spectra, and the total size of the data. In addition, it can create 2D-plot graphics of the m/z values vs. time for QA purposes.
Language:C#8 7 13
Thermo-Raw-File-Reader
.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific
Language:C#38 16 211

Computational Mass Spectrometry @ Pacific Northwest National Laboratory's Repositories

PNNL-Comp-Mass-Spec/Thermo-Raw-File-Reader
.NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific
Language:C#38 16 211
PNNL-Comp-Mass-Spec/DeconTools
Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
Language:C#17 21 74
PNNL-Comp-Mass-Spec/MASIC
MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis, characterizing the peak(s) in each SIC, computing peak statistics including elution time of the peak apex, peak area, and peak signal/noise. It can also extract reporter ion abundances (e.g. iTRAQ or TMT).
Language:C#15 6 54
PNNL-Comp-Mass-Spec/DB-Schema-Export-Tool
Exports SQL Server and Postgres database objects as schema files. Exported objects include tables, views, stored procedures, and functions, plus also database properties including database roles and logins. The program can also export table data to create SQL files with an Insert Into statement for each row.
Language:C#12 6 27
PNNL-Comp-Mass-Spec/MS-File-Info-Scanner
Examines a series of MS data files (or data directories) and extracts the acquisition start and end times, number of spectra, and the total size of the data. In addition, it can create 2D-plot graphics of the m/z values vs. time for QA purposes.
Language:C#8 7 13
PNNL-Comp-Mass-Spec/AScore
The AScore program can process first-hits or synopsis files from MS-GF+, SEQUEST, or X!Tandem to compute confidence scores for the position of phosphorylated residues.
Language:C#3 5 01
PNNL-Comp-Mass-Spec/DBSchema_DMS
PRISM Data Management System database schema
Language:TSQL3 11 03
PNNL-Comp-Mass-Spec/DBSchema_PgSQL_DMS
PRISM Data Management System PostgreSQL database schema
Language:PLpgSQL3 5 0
PNNL-Comp-Mass-Spec/DMS-Analysis-Manager
DMS Analysis Tool Manager
Language:C#3 8 0
PNNL-Comp-Mass-Spec/MyEMSL-Reader
MyEMSL Reader
Language:C#2 9 0
PNNL-Comp-Mass-Spec/PRISM-Class-Library
The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.
Language:C#2 11 02
PNNL-Comp-Mass-Spec/DMS-Capture-Task-Manager
DMS Capture Task Manager
Language:C#1 8 0
PNNL-Comp-Mass-Spec/DMS-Website
DMS Website
Language:PHP1 10 0
PNNL-Comp-Mass-Spec/PNNL.DMS.utils
Tools to interface with PNNL's DMS in R
Language:R1 6 180
PNNL-Comp-Mass-Spec/UIMF-Library
Used to create, modify and extract data from UIMF files, which are SQLite databases of mass spectrometry data acquired at Pacific Northwest National Laboratory (PNNL)
Language:C#1 24 24
PNNL-Comp-Mass-Spec/Buzzard
Utility for manually and automatically adding datasets to DMS
Language:C#10 0
PNNL-Comp-Mass-Spec/Cyclops
The Cyclops library can be used to apply a workflow of data analysis steps to data stored in a SQLite database
Language:C#5 0
PNNL-Comp-Mass-Spec/Data-Import-Manager
DataImportManager (DIM)
Language:C#10 0
PNNL-Comp-Mass-Spec/DataPackage-Archive-Manager
DataPackage Archive Manager
Language:C#10 0
PNNL-Comp-Mass-Spec/DLL-Version-Inspector
This program inspects a .NET DLL or .Exe to determine the version. This allows a 32-bit .NET application to call this program via the command prompt to determine the version of a 64-bit DLL or Exe.
Language:C#4 0
PNNL-Comp-Mass-Spec/DMS-Instrument-Directory-Scanner
Instrument directory scanner
Language:C#9 0
PNNL-Comp-Mass-Spec/DMS-Organism-Database-Handler
Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application
Language:C#9 01
PNNL-Comp-Mass-Spec/DMS-Space-Manager
DMS Space Manager
Language:C#9 0
PNNL-Comp-Mass-Spec/DMS-Update-Manager
DMS Update Manager
Language:C#10 0
PNNL-Comp-Mass-Spec/Interference-Detection
Algorithm for quantifying the homogeneity of species isolated for fragmentation in LC-MS/MS analyses using data directed acquisition (DDA).
Language:C#5 0
PNNL-Comp-Mass-Spec/Mage
The Mage suite of tools provide access to DMS files and metadata.
Language:C#23 0
PNNL-Comp-Mass-Spec/Package_Folder_Create_Manager
Creates a new storage folder for newly created data packages
Language:C#10 0
PNNL-Comp-Mass-Spec/PNNL.DIA.utils
**WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects
Language:R3 01
PNNL-Comp-Mass-Spec/Status-Message-DB-Updater
Reads manager status messages from an ActiveMQ server and push them into the DMS database.
Language:C#5 0
PNNL-Comp-Mass-Spec/VSProj-NuGet-Version-Updater
Searches for Visual Studio project files (.csproj and.vsproj) that reference a specific NuGet package and updates the referenced version to a newer version if necessary.
Language:C#5 0