Whole Cell MALDI Fingerprinting Is a Robust Tool for Differential Profiling of Two-Component Mammalian Cell Mixtures

Abstract

MALDI fingerprinting was first described two decades ago as a technique to identify microbial cell lines. Microbial fingerprinting has since evolved into an automated platform for microorganism identification and classification which is now routinely used in clinical and environmental sectors. The extension of fingerprinting to mammalian cells has yet to progress partly due to compartmentalization of eukaryotic cells and overall higher cellular complexity. A number of publications on mammalian whole cell fingerprinting suggests that the method could be useful for classification of different cell types, cell states, and monitoring cell differentiation. We report the optimization of MALDI fingerprinting workflow parameters for mammalian cells and its application for differential profiling of mammalian cell lines and two component cell line mixtures. Murine fallopian tube cells and high-grade ovarian carcinoma cell lines and their mixtures are used as model mammalian cell lines. Two-component cell mixtures serve to determine the method's feasibility for complex biological samples as the ability to detect cancer cells in a mixed cell population. The level of detection of cancer cells in the two-component mixture by principle component analysis (PCA) starts to deteriorate at 5% but with application of a different statistical approach, Wilcoxon rank sum test, the level of detection was determined to be 1%. The ability to differentiate heterogeneous cell mixtures will help further extend whole cell MALDI fingerprinting to complex biological systems.

An integrated approach to protein discovery and detection from complex biofluids

“…has previously optimized a method for the detection of microproteins from a more complex biofluid (i.e. whole cell cultures) in which a mixture of cells are present and analyzed using MALDI-TOF protein profiling 12 . A follow up study by Galey et al .…”

“…Petukhova et al has previously optimized a method for the detection of microproteins from a more complex biofluid (i.e. whole cell cultures) in which a mixture of cells are present and analyzed using MALDI-TOF protein profiling 12 . A follow up study by Galey et al used MALDI-TOF MS protein profiling to identify features that are differentially expressed over time as tumor burden increased in murine vaginal lavages 11 .…”

“…high grade serous ovarian cancer, a prominent and particularly fatal subtype of ovarian cancer; HGSOC) or in the uterus (i.e. endometrial cancer) may escape and concentrate earlier than in serum [12][13][14] .…”

Intact Cell Mass Spectrometry for Embryonic Stem Cell Biotyping

“…Principal component analysis then revealed informative peaks for deeper spatial analysis using mass spectrometry imaging in whole brain sections. Similarly, mass spectra have demonstrated to contain sufficient information to reveal the immunophenotype and activation state of immune cells, [42][43][44][45] or to classify distinct mammalian cell lines [46,47]. Moreover, MS can reveal changes associated with molecular phenotype, which occur within cell lines and sublines of common genetic origin.…”

Profiling embryonic stem cell differentiation by MALDI TOF mass spectrometry: development of a reproducible and robust sample preparation workflow

“…30 This study enabled the identification of 520 lipid features and classification of neuron-like and astrocyte-like cells, thus allowing lipid profiles to be assigned to particular cellular functions. Characterising the protein signatures of mammalian cells by MALDI-MS is less common when compared with lipid analysis; however it has been used for phenotypic screening of human cancer cell lines, 31,32 identification of cells within a co-culture 33,34 or tissues 35 and detection of transient changes within a specific cell type, such as immune cells. [36][37][38][39] However, many of these studies list dramatically different experimental procedures with several being adapted from existing biotyping protocols.…”