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

IMP Spectrum Analyzer

The Spectrum Analyzer Software was designed to analyze .raw files to provide complete information about the spectra. The collected data is output in a .txt file (comma separated values), which can easily be loaded into calculation software, such as Excel or R, where it can be further processed. For each input .raw file an output file with the name [.raw file name]-analysis.txt is created.

The following data is collected:

General Spectrum Information:
o Spectrum Number
o Retention Time
o Precursor Spectrum Number
o Precursor m/z
o Collision Energy in eV
o Isolation width
o Low mass
o High mass
o Cycle Time
o Scans after last MS1 scan
o Cycle time

Precursor Information (for both MS1 and MS2 scans):
o Ion Injection Time
o TIC (Total Ion Current)
o Intensity
o Noise
o Signal to Noise
o Total Intensity in isolation window
o Total intensity in the whole scan
o PIF (Precursor Intensity Fraction):
      MS1: Precursor Intensity / Sum of Intensities in isolation window
      MS2: Precursor Intensity / Sum of Intensities in whole MS2 scan
o Precursor Isolation Efficiency:
      = Precursor intensity in MS2 spectrum / Precursor intensity in MS1 spectrum.
      This only yields useful results if the precursor is not fractioned.

Reporter Ion Information:
o Deviation in ppm
o Intensity
o Noise
o Signal to Noise
o Number of reporter ions found
o Total intensity of the reporter ions

Elution Profile Information:
o Area
o Apex Intensity
o Apex Retention Time



Spectrum Analyzer(720 KB Zip Archive)

Spectrum Analyzer was invented and coded by Frederico Duisberger and inspired by various MassSpec group members.