Mass spectrometry, Protein Chemistry Facility
Research Institute of Molecular Pathology (IMP)
Institute of molecular biotechnology of the Austrian Academy of Sciences (IMBA)
Gregor Mendel Institute of Molecular Plant Biology (GMI)

PD-Nodes SimpatiQCo Software Tools Publications

MS2 Spectrum Processor, v. 0.9

This software has been developed to be used with the Thermo Scientific Proteome Discoverer software, versions 1.3.x, 1.4.x and 2.1.x. It adds a new node that can be incorporated into the workflow allowing the execution of the following two MS2-spectrum preprocessing steps:


Simply include the MS2 – Sepctrum Processor node into a workflow, preceded by a Spectrum Source (e.g. Spectrum Selector or another spectrum manipulation node) and followed by the search node, or another spectrum manipulation node.

Workflow example


We analysed the performance of the MS2-Spectrum Processor node for two HCD HeLa samples (both 1 μg) which were run on a QExactive and a Velos Orbitrap.
The following chart shows a comparison in the obtained results regarding the Peptide Spectrum Matches (PSMs) and the Peptide Identifications at 1% FDR.

Performance Chart

The resulting .msf-files generated by Thermo Scientific Proteome Discoverer can be downloaded here:

In the following table the corresponding filter settings that were used in Proteome Discoverer to achieve the 1% FDR for PSMs, as well as Peptide Identifications are listed:

QEx, no Preprocessing QEx, with Deisotoping and Deconvolution Velos, no Preprocessing Velos, with Deisotoping and Deconvolution
PSMs Peptide Identifications PSMs Peptide Identifications PSMs Peptide Identifications PSMs Peptide Identifications
Lowest Peptide Length 8 8 8 8 8 8 8 8
Search Engine Rank 1 1 1 1 1 1 1 1
Peptide Score (Mascot) 5.83 8 5.44 7.67 3.95 7.5 4.09 7.3

Download and installation

For Proteome Discoverer 2.1 use the installer found here