MALDI versus ESI: The Impact of the Ion Source on Peptide Identification

Abstract

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.

Elucidation of chemical modifier reactivity towards peptides and proteins and the analysis of specific fragmentation by matrix‐assisted laser desorption/ionization collision‐induced dissociation tandem mass spectrometry

“…Fragment ion mass spectra exhibited indicative signals which could be assigned to specific elimination processes and neutral losses as an alternative or even excusive fragmentation pathway to the usual b−/y‐fragmentation. Our findings are in agreement with the recently published article by Nadler et al who described a better PTM analysis with ESI‐MS in comparison with MALDI‐MS. Additionally, we provide evidence for the hypothesis that modified peptides undergo a different fragmentation mechanism in MALDI‐MS which is not covered by common search algorithms.…”

“…The analysis of chemical modifications of proteins is nowadays studied by mass spectrometry. While electrospray ionization (ESI)‐MS was described to perform well for hydrophobic, modified, and terminal lysine‐containing peptides, the use of matrix‐assisted laser desorption/ionization (MALDI)‐MS is advantageous for studying small basic and thus highly charged (> 2+/3+) peptides containing histidine and those possessing a terminal arginine . However, to determine the position of chemical modifications, modified peptides are in most cases analyzed using ESI‐MS.…”

2D Electrophoretic pattern of bovine placental proteins during early‐mid pregnancy

“…Both techniques are complementary and allow for the much more precise and complete identification of proteins. 19,20 In the case of nano-LC-MS/MS technique, the analysis was…”

“…Our previous paper applied analytical system based on the application of TRIS buffer for protein isolation and a nano LC‐MS/MS system, while the present one considers proteins, which differ in solubility (isolation in phosphate buffer), and protein separation was performed with the aid of 2D electrophoresis, followed by MALDI TOF/TOF MS analysis. Both techniques are complementary and allow for the much more precise and complete identification of proteins . In the case of nano‐LC‐MS/MS technique, the analysis was preceded by the one dimensional SDS PAGE, and the obtained peptide mixture was separated on the nanochromatographic column what allowed for the identification of proteins, even if they were overlapping in the gel bands.…”

Tear Proteins Calcium binding protein A4 (S100A4) and Prolactin Induced Protein (PIP) are Potential Biomarkers for Thyroid Eye Disease

“…In their study, MALDI-TOF/TOF was used for protein identification, which is different from our LC-ESI-MS/MS. Due to different proteomics platform used, there could be study-specific biomarkers identified in each study 22 . However, in our current study, the two biomarker candidates were identified from two independent cohorts using two different techniques (iTRAQ and SWATH).…”