MALDI versus ESI: The Impact of the Ion Source on Peptide Identification.
For mass spectrometry-based proteomic analyses, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are the commonly used ionization techniques. To investigate the influence of the ion source on peptide detection in large-scale proteomics, an optimized GeLC/MS workflow was developed and applied either with ESI/MS or with MALDI/MS for the proteomic analysis of different human cell lines of pancreatic origin. Statistical analysis of the resulting data set with more than 72 000 peptides emphasized the complementary character of the two methods, as the percentage of peptides identified with both approaches was as low as 39%. Significant differences between the resulting peptide sets were observed with respect to amino acid composition, charge-related parameters, hydrophobicity, and modifications of the detected peptides and could be linked to factors governing the respective ion yields in ESI and MALDI.
German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Wiebke Maria
0000-0002-7673-1147
WM
Nadler
SCIEX Germany GmbH , Landwehrstraße 54, 64293 Darmstadt, Germany.
Dietmar
D
Waidelich
German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Alexander
A
Kerner
German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Sabrina
S
Hanke
Department of Chemistry, University of Zurich , Winterthurerstr. 190, 8057 Zurich, Switzerland.
Regina
R
Berg
German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Andreas
A
Trumpp
German Cancer Research Center and HI-STEM gGmbH , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
Christoph
C
Rösli
D000596:Amino Acids; D002460:Cell Line; D045744:Cell Line, Tumor; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D010179:Pancreas / Q000166:cytology; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000295:instrumentation* / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000295:instrumentation* / Q000379:methods
D000596:Amino Acids; D010455:Peptides
ESI; MALDI; ionization; peptide modification; proteomics