Physikron`s Leaflet

The results
By multiplying the number of secondary spectra by a factor between 2 and 5, Physikron technology
increases the MS/MS throughput by the same factor. Fragments that correspond to a specific primary
mass are filtered. As a result, the gain in the number of identified proteins by Physikron technology reaches
between 25% and 80% (depending on the type of spectrometer used and the complexity of the sample).
Histogram of the number of proteins coming from the same Human Cells sample:
an example of the performance of the Physikron technology.
As example of the performances of the Physikron technology, figure 1
represents the histogram of the number of proteins coming from the same
Human Cells sample. The mass spectrometer used is a LC-ESI-LTQ-Orbitrap
Velos (Thermo Fisher) and the search engine is Mascot.
NUMBER OF
IDENTIFIED
PROTEINS
1385 proteins
82%
Figure 1: Gain achieved on the identification of proteins thanks to Physikron Technology.
1 μg of a human cell lysates sample was analyzed (trypsin digest). The instrument
used is a LC-ESI-LTQ-Orbitrap Velos in HCD MS-MS mode. The acquisition time was of
3 hours (HPLC). The precision was of 4 ppm for the MS data produced (30000 MS
resolution) and 10 ppm for the MS/MS data produced (7500 MS-MS resolution). The
search engine was Mascot (SwissProt) the mass spectrometer was a LC-ESI-LTQOrbitrap Velos (Thermo Fisher) and the search engine Mascot.
STANDARD
MASCOT
ANALYSIS
MASCOT
ANALYSIS
WITH
PHYSIKRON
TECHNOLOGY
FDR = 0.85%
FDR = 0.9%
762 proteins
Number of proteins identified from a standard and Physikron analysis compared as a function of
the precursor mass window width. MS/MS data shown on the plot are produced from a Human Cell
sample by a LC-ESI-LTQ-Orbitrap Velos (Thermo Fisher) in the MS/MS HCD high resolution mode.
On figure 2, the number of proteins identified from a standard and Physikron
analysis are compared as a function of the precursor mass window width.
MS/MS data shown on the plot are produced from a Human Cell sample
by a LC-ESI-LTQ-Orbitrap Velos (Thermo-Fisher) in the MS-MS HCD high
resolution mode.
NUMBER OF
IDENTIFIED
PROTEINS
HCD LC-MS-MS DATA PRODUCED BY AN LC-ESI-LTQ-ORBITRAP VELOS
HUMAN CELL 2 SAMPLE 1 μg WITH TRYPSIN DIGEST HPLC 3 HOURS
MS RESOLUTION 30000, MS-MS RESOLUTION 7500
STANDARD MASCOT ANALYSIS FDR < 1%
MASCOT ANALYSIS WITH PHYSIKRON TECHNOLOGY FDR < 1%
1500
1385
1117
82%
21%
1000
1038
921
762
500
324%
245
Figure 2: Evolution of the number of proteins identified according to the width of the
selection window for the precursor mass
3 Da
6 Da
12 Da Precursor mass
window width
ÎPhysikron technology with the Velos HCD high resolution mode identifies more proteins than the standard LTQ low
resolution mode. It allows for the advantages of HCD standard mode (high resolution with small mass fragments
are not detected in LTQ mode).