Skip to content
@PNNL-Comp-Mass-Spec

Computational Mass Spectrometry @ Pacific Northwest National Laboratory

Repositories

  • 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).

    C# 1 6 1 0 Updated Nov 26, 2020
  • MASIC-Results-Merger

    Merges the contents of a tab-delimited text file with peptide search results (e.g. from X!Tandem or MSGF+) with the corresponding MASIC results files, appending the relevant MASIC stats for each PSM. Also supports reporter ion abundances.

    C# 0 1 0 0 Updated Nov 26, 2020
  • DMS-Analysis-Manager

    DMS Analysis Tool Manager

    C# BSD-2-Clause 0 1 0 0 Updated Nov 25, 2020
  • DMS-Capture-Task-Manager

    DMS Capture Task Manager

    C# BSD-2-Clause 0 0 0 0 Updated Nov 25, 2020
  • 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.

    C# 2 2 1 0 Updated Nov 25, 2020
  • Thermo-Raw-File-Reader

    .NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific

    C# 6 13 1 0 Updated Nov 24, 2020
  • PPMErrorCharter

    Utility for generating plots of the mass measurement errors before and after processing with mzRefinery

    C# 0 0 0 0 Updated Nov 23, 2020
  • LCMSNet

    LCMSNet software for instrument control

    C# 1 1 0 0 Updated Nov 22, 2020
  • DBSchema_DMS

    PRISM Data Management System database schema

    TSQL 3 2 0 0 Updated Nov 21, 2020
  • Interference-Detection

    Algorithm for quantifying the homogeneity of species isolated for fragmentation in LC-MS/MS analyses using data directed acquisition (DDA).

    C# 0 0 0 0 Updated Nov 21, 2020
  • PNNL-Omics

    Data analysis, file I/O, and visualization routines used by several of the omics-related software developed at PNNL

    C# 1 0 0 0 Updated Nov 21, 2020
  • DMS-Website

    DMS Website

    PHP 0 0 0 0 Updated Nov 20, 2020
  • DeconTools

    Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.

    C# 3 9 1 0 Updated Nov 20, 2020
  • MyEMSL-Reader

    MyEMSL Reader

    C# 0 2 0 0 Updated Nov 18, 2020
  • InfernoRDN

    InfernoRDN can perform various downstream analyses on large scale datasets from proteomics and microarrays

    C# 2 3 1 0 Updated Nov 18, 2020
  • 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.

    C# 2 1 0 0 Updated Nov 17, 2020
  • DBSchema_MTS

    PRISM Mass and Time Tag System database schema

    TSQL 2 2 0 0 Updated Nov 14, 2020
  • UIMF-Viewer

    Visualization software for IMS data stored in a UIMF file

    C# 0 1 0 0 Updated Nov 14, 2020
  • Buzzard

    Utility for manually and automatically adding datasets to DMS

    C# 0 0 0 0 Updated Nov 13, 2020
  • protein-coverage-summarizer

    Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

    C# BSD-2-Clause 2 1 0 0 Updated Oct 31, 2020
  • 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.

    C# 0 0 0 0 Updated Oct 30, 2020
  • Thermo-Peak-Data-Exporter

    Extracts peak intensity data from each scan in a Thermo raw file, and writes that data to a tab-delimited text file.

    C# 0 0 0 0 Updated Oct 28, 2020
  • Protein-File-Reader

    Class for reading Protein files, specifically .fasta files and certain tab-delimited formats

    C# 1 0 0 0 Updated Oct 27, 2020
  • Protein-Digestion-Simulator

    Performs validation, transformation, and in-silico digestion of text files containing protein or peptide sequences (FASTA format or delimited text)

    Visual Basic .NET 1 2 0 0 Updated Oct 23, 2020
  • SMAQC_Website

    CodeIgniter based website for browsing QC Metrics stored in DMS

    HTML MIT 0 0 0 0 Updated Oct 21, 2020
  • uimfpy

    UIMF python library

    Python 3 1 0 1 Updated Oct 21, 2020
  • IMS-Drift-Time-Aligner

    Processes IMS data in a UIMF file to align all frames to a base frame, adjusting the observed drift times of each frame to align with the base frame.

    C# 0 1 0 0 Updated Oct 16, 2020
  • mediawiki-extensions-LdapAuthentication

    Forked from wikimedia/mediawiki-extensions-LdapAuthentication

    Github mirror of MediaWiki extension LdapAuthentication - our actual code is hosted with Gerrit (please see https://www.mediawiki.org/wiki/Developer_access for contributing)

    PHP GPL-2.0 11 0 0 0 Updated Oct 15, 2020
  • DB-Schema-Export-Tool

    Exports Sql Server 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.

    C# BSD-2-Clause 2 4 0 0 Updated Oct 12, 2020
  • R 2 0 0 0 Updated Oct 2, 2020

Top languages

Loading…

Most used topics

Loading…

You can’t perform that action at this time.