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Multiplex LC-MS analysis to selectively detect different collagen types in fibrotic tissue
Anne [email protected]
15 November 2017
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Contents
Introduction
Collagen types, method design and development
Results pilot study
Conclusions & Future
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Triskelion general workflow
1. Sample purification / pre-processing
2. Analyte processing
3. Liquid Chromatography – Mass Spectrometry (LC-MS)
4. Target selection and internal standardization strategy (parallel phase)
The workflow has been applied in many different protein LC-MS method developments (pharma & food)
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1. Sample purification / pre-processing
No sample purification
Less/moderately selective purification:Precipitation, SPE, depletion, SDS-PAGEProtein A/G/L, immobilized receptor
Highly selective purification:Anti-idiotype antibody
SolubilizationHarsh chemical conditions, solvent, pH, reductor, surfactantSonicationTemperature
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2. Analyte processing
None => Intact / Top down
Removal of groups, such as sugar / payload
Denaturation => make protein accessible to further processing
Reduction => cleave S-S bridges
Alkylation => modify free SH
Digestion => Release signature or generic peptide
Modify initial analyte to detection target
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3. LC-MS
Liquid chromatography several options:Injection conditionsStationary and mobile phasesColumn dimensions
Mass spectrometry several options:Ionization, e.g. ESIAnalyzer, e.g. triple quad, OrbitrapTandem MS
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4. Target selection and internal standardization strategy
Theoretical target selection criteria
Experimental target selection criteria
Stable isotope labeled internal standard (SIL IS) peptide vs. SIL IS protein vs. combined internal standardization (non-labeled protein + SIL IS peptide)
Preferably 13C / 15N as stable isotopes
SIL IS facilitates peak assignment in complex chromatograms
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Method development (1)
Aim of the study: development of a method to selectively detect collagen types in lung tissue to support fibrosis research
Methods requiring free protein or protein 3D structure not suitable => Bottom up LC-MS
Challenges:Solubilize crosslinked collagenIdentify selective targets for murine collagen types (1, 3-6)
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Solubilization
Trifluoroacetic acid (TFA) necessary to solubilize crosslinked collagen, however subsequent precipitation.
Other tested conditions: 0.1% Rapigest, heating, sonication, grinding, cutting, Dissociator treatment, ultraturrax, 0.1% Tween-20, and combinations of these conditions.
Crucial step: pretreatment with ammonia. Pellet appearance from white to more transparent.
Method development (2)
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Digestion (1)
Initially no LC-MS/MS identifications after digestion with trypsin in 100 mM ABC (slightly basic conditions). Pepsin digestion did provide identifications (acidic conditions).
TFA inhibits trypsin? Modified lysines impair tryptic digestion?
Disadvantage of pepsin: rather non-specific. Trypsin is highly preferred due to its compatibility with LC-MS:
Suitable mass range for MS(/MS) detectionBasic residue in cleaved peptides (K or R): protonation
Method development (3)
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Method development (4)
Digestion (2)
Trypsin is even more desired in collagen analysis. K and R occur at regular intervals.
Homo sapiens
Collagen 1α1Helical domain
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Method development (5)
Digestion (3)
Trypsin is even more desired in collagen analysis.K and R are conserved amino acids.
Codon group involvement in changes between
Homo sapiens&
Mus musculus
Collagen 1α1Helical domain
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Method development (6)
Digestion (4)
Only after ammonia pre-treatment suitable tryptic digestion was observed
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Method development (7)
Target selection
Theoretical target selection using selection criteria and database search. Experimental target selection using qualitative LC-MS Orbitrap.
Color range per target
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Method development (8)
Targets were assigned for murine collagens 1α1, 3α1, 4α1, 5α1 and 6α2
Method transfer to triple quadrupole LC-MS/MS
Target structure confirmation using Orbitrap MS/MS data, collagen peptide example:
SIL IS synthesis VGApGPAGARDuck collagen 1α2
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Pilot study (1)
Lung lobe wet weight (mg +/- 1 sd)Collagen content (µg)
Hyp assay
Lung fibrosis was induced in 12-week old male C57Bl/6 mice by oropharyngeal administration of bleomycin
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Pilot study (2)
Collagen type (ratio analyte / SIL IS)
Collagen type normalized to PBS group
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ConclusionsThe developed LC-MS methodology allows the investigation of changes in collagen composition in murine lung.
First step to better defined disease analysis (fibrosis).
Collagen types exhibit different behavior after bleomycin exposure.
FutureDetermine the extracted fraction by analysis of hydroxyproline in supernatant and pellet fractions.
Further method qualification. Obtain pure collagen types?
Other tissues / disease states (e.g. liver / NASH).
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Acknowledgements
Frédérique van HolthoonBiomolecular MS group
Reinout Stoop Joline AttemaChrista de Ruiter
Sarah Brockbank
Animal species specific quantification of gelatin