Suppression effects in peptide mapping by plasma desorption mass spectrometry

Area of Science:

• Analytical Chemistry
• Biochemistry
• Mass Spectrometry

Background:

• Suppression effects are a known phenomenon in mass spectrometry, impacting quantitative analysis.
• Plasma desorption (PD) and fast atom bombardment (FAB) mass spectrometry are ionization techniques used for analyzing biomolecules.

Purpose of the Study:

• To investigate and compare the suppression effects in PD mass spectrometry (PDMS) and FAB mass spectrometry.
• To elucidate the fundamental differences in the suppression mechanisms between PDMS and FAB.
• To explore the utility of PDMS suppression characteristics for protein analysis.

Main Methods:

• Comparative analysis of suppression effects in PDMS and FAB mass spectrometry.
• Investigation of ion detection behavior based on charge in positive and negative ion modes of PDMS.
• Application of PD mapping with enzymatic digestion for protein coverage analysis.

Main Results:

• A fundamental difference in suppression mechanisms between PDMS and FAB was demonstrated.
• In positive ion mode PDMS, peptides with net positive charges are preferentially detected over those with net negative charges.
• In negative ion mode PDMS, the detection preference is generally reversed, showing complementarity.

Conclusions:

• The charge-dependent detection in PDMS, unlike FAB, offers a complementary approach for analyzing complex peptide mixtures.
• PD mapping, leveraging enzymatic digestion and the complementary nature of PDMS, can achieve almost complete coverage of smaller proteins.
• Understanding and utilizing suppression effects in PDMS enhances its applicability in proteomic studies.