PD Nodes

PD-Nodes is a collection of nodes designed for Thermo Scientific Proteome Discoverer.
It will grow over time and give developers a platform and users the possibilty to download and use new interesting nodes.

IMP Nodes Collection
Collection of the IMP Nodes for PD 2.1 and 2.3
A collection of software tools (Nodes) which enable the automated identification of intact glycopeptides from HCD‐MS/MS data sets.
Enables automated and confident localization of phosphorylation sites within validated peptide sequences and can be applied to all commonly used fragmentation techniques (CID, ETD and HCD).
Is the successor of PhoshoRS.
Label-free quantification for Discoverer.
MS2 Spectrum Processor
Deisotoping of isotopic clusters and charge deconvolution.
MS Amanda
A high-speed identification and scoring system for peptides out of tandem mass spectrometry data using a database of known proteins. Especially designed for high resolution and high accuracy tandem mass spectra.
A workflow that allows for deeper insights into tandem mass spectra by enabling the identification and validation of chimeric spectra using retention time prediction.
MS Ana
A scoring system to identify peptides in tandem mass spectrometry data using a library of previously identified spectra. Able to create decoy spectral libraries that are to allow for validation of results using the target-decoy approach.
MS Annika
A cross-linking search engine for use with cleavable cross-linkers and MS2 or MS2-MS3 spectra. Able to deal with a wide variety of cleavable cross-linkers and provides robust and transparent FDR control based on a target-decoy approach.
IMP Hyperplex
A node for quantifying labelling ions, like TMT, TMTc ("complementary" TMT reporters) or EASI-tag ions.
Post-Search Calibrator Node
Performs a recalibration of the precursor masses based on the results of a previous search.
Spectrum merger Node and Standalone version
Can be used to consolidate .raw files where separate id- and quan-scans have been recorded for each precursor.
Spectrum filter Node
A tool to generate patterns from PSMs with posttranslational Modifications.
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