TY  - JOUR
AU  - Li, Mujia Jenny
AU  - Meyer, Larissa Chiara
AU  - Meier, Nadine
AU  - Witte, Jannik
AU  - Maldacker, Maximilian
AU  - Seredynska, Adrianna
AU  - Schueler, Julia
AU  - Schilling, Oliver
AU  - Föll, Melanie Christine
TI  - Spatial Proteomics by Parallel Accumulation-Serial Fragmentation Supported MALDI MS/MS Imaging: A First Glance Into Multiplexed and Spatial Peptide Identification.
JO  - Rapid communications in mass spectrometry
VL  - 39
IS  - 9
SN  - 0951-4198
CY  - New York, NY
PB  - Wiley Interscience
M1  - DKFZ-2025-00301
SP  - e10006
PY  - 2025
AB  - In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurements. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of tryptic peptides to enable multiplexed MS/MS imaging.An initial MALDI TIMS MS1 survey measurement was performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors were trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors were identified by peptide to spectrum matching.This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability was showcased on two histomorphologically distinct tissue specimens in a four-plex and five-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.In this study, we present a novel pipeline, based on iprm-PASEF, that allows the multiplexed and spatial identification of tryptic peptides in MALDI imaging. Hence, it marks a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
KW  - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization: methods
KW  - Proteomics: methods
KW  - Tandem Mass Spectrometry: methods
KW  - Animals
KW  - Peptides: chemistry
KW  - Peptides: analysis
KW  - Ion Mobility Spectrometry: methods
KW  - Peptide Fragments: analysis
KW  - Peptide Fragments: chemistry
KW  - MALDI imaging (Other)
KW  - MS/MS imaging (Other)
KW  - TIMS (Other)
KW  - iprm‐PASEF (Other)
KW  - peptide imaging (Other)
KW  - spatial proteomics (Other)
KW  - Peptides (NLM Chemicals)
KW  - Peptide Fragments (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:39910729
DO  - DOI:10.1002/rcm.10006
UR  - https://inrepo02.dkfz.de/record/298584
ER  -