A.

NEW DEPTHS OF ANALYSIS OF COMPLEX PROTEOMICS SAMPLES

High performance mass spectrometers with extreme sensitivity and resolution have illuminated a need for improved on-the-fly spectral analysis and peak assignment. The Advanced Peak Determination (APD) algorithm fills this need by identifying the charge states and monoisotopic m/z values of isotopic envelopes at greatly improved peak depths. This algorithm dramatically increases the population of precursors available for data-dependent analysis, which in turn results in more MS2 spectra, PSMs, and unique peptide identifications.

STANDARD PEAK DETERMINATION

ADVANCED PEAK DETERMINATION

Thermo Scientific Orbitrap FusionLumos Tribrid Mass Spectrometerwith Advanced Peak Determination

EquivalentIDs in halfthe time

Advanced PeakDetermination

Standard PeakDetermination

More IDs inthe same time

Uni

que

pep

tides

, <1%

FDR

60,000

50,000

40,000

30,000

20,000

10,000

060 min 120 min 60 min 120 min

469.0 469.5 470.0 470.5 471.0 471.5 472.0 472.5

m/z

469.750z=?

469.899z=? 470.251

z=?470.735

z=?471.236

z=?470.567z=? 471.737

z=?470.901

z=?468.879

z=?472.773

z=?472.238

z=?469.213

z=?

469.750z=2

469.899z=3

470.233z=3 470.735

z=2

471.236z=2470.567

z=3471.737

z=2470.899

z=3468.879

z=3472.238

z=2469.214

z=3469.54888

z=3472.774

z=2

No precursors determined

Precursor 1 Precursor 2

Precursor 3

469.0 469.5 470.0 470.5 471.0 471.5 472.0 472.5

m/z

469.750z=?

469.899z=? 470.251

z=?470.735

z=?471.236

z=?470.567z=? 471.737

z=?470.901

z=?468.879

z=?472.773

z=?472.238

z=?469.213

z=?

469.750z=2

469.899z=3

470.233z=3 470.735

z=2

471.236z=2470.567

z=3471.737

z=2470.899

z=3468.879

z=3472.238

z=2469.214

z=3469.54888

z=3472.774

z=2

No precursors determined

Precursor 1 Precursor 2

Precursor 3

Reading Between the Lines with Advanced Peak Determination

Advanced Peak Determination allows for real-time assignment of a significantly larger number of charge states and monoisotopic peaks in complex MS spectra in comparison with Standard Peak Determination. This results in a corresponding increase in MS/MS data-dependent events, PSMs, unique peptide and protein identifications.

The Thermo Scientific™ Orbitrap Fusion™ Lumos™ Tribid™ MS with Advanced Peak Determination, in conjunction with LC-MS/MS methods that leverage the low detection limits of the MS and incredibly high ion trap MS/MS scan rates, significantly boosts the rate of unique peptide identifications, shown here with a 1 µg HeLa digest analyzed using 1 h and 2 h gradients (n=3).

www.planetorbitrap.com/orbitrap-fusion-lumos

Advanced Peak Determination is an optional Global MS property of the Method Editor.

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Find out more at thermofisher.com/lumos

“The new APD algorithm provides new peptide precursors to go after and amounts to a 25–35% identification bonus. I have no doubt this will be a key technology in achieving deeper coverage and higher throughput for proteome analyses.”

—Josh Coon, Professor, The University of Wisconsin-Madison