How can complex biological matrices impact results for analytical methods, especially pyrolysis GC/MS? How can methods to "clean up" or "remove" biological matrices impact results for pyrolysis?

The presence of biopolymers in sample extracts can impede the performance of spectroscopic techniques such as micro-FT-IR, as the spectra of MNPs and biopolymers have similarities. Likewise, the ions used by py-GC-MS to measure MNPs can also arise from biopolymers. I am not aware that methods to clean up biological matrices can impact results obtained  via pyrolysis.

The presence of organic matter can saturate the pyrolysis chamber, leading to poor resolution and co-elution of pyrolysates. Complex matrices, such as biological matrices, may generate high background, reducing signal-to-noise ratio, making it harder to detect low-abundance polymers. Pyrolysis products can also mimic or mask plastic-derived signals, affecting identification. The used clean up methods, such as enzymatic or oxidative digestion, may, if incomplete, leave interfering residues, but, if too harsh, degrade sensitive polymers. Other methods, such as solvent extraction, can result in the dissolution of lower density polymers.  

Biological matrices are generally rich in natural substances lipids, proteins, sugars. These substances can affect Py-GC/MS in several ways:

1 – By producing pyrolysis fragments (e.g. amides, ketones, fatty acids) that can overlap with plastic pyrolysis markers. This creates false positives or misidentifications.

2 – By co-elution of biological pyrolysis products with plastic monomers, especially for polyamide, PET, PVC.

3 – By increasing background noise, raising the baseline and reducing the signal-to-noise ratio. This will make detection of MNPs harder, especially the low-abundance ones.

4 – By contaminating the pyrolysis unit of the GC column. This will reduce sensitivity.

5 – By inducing non-reproducible signal intensities, skewing semi-quantitative results.

Methods to "clean up" or "remove" biological matrices can impact results for pyrolysis in various ways and lead to various concerns:
1 – Plastics may degrade in full or partly and this sample loss during cleanup will lead to underestimation of the actual plastics content.

2 – Incomplete digestion may introduce biological pyrolysates which lead to false positives.
3 – Filtering of the substrate might induce background contamination. This may also be due to pyrolysis of the filter material.

4 – Residual water or salts may affect the thermal behavior in some of the subsequent analysis steps and induce baseline noise.

Complex biological matrices can affect considerably  the precision, and interpretability of  the data obtained from  from PyGC/MS when used to analyze microplastics. In the case of pyrolysis GC/MS particularly, the biological matrices  can produce background signals during pyrolysis which can mimic or overlap with the  analyzed sample's  peaks, thus leading to a misinterpretation of the results. Also, during pyrolysis, the biological matrices constituents could degrade and produce volatile compounds, which can also interfere with the identification of the polymers or compounds. Depending on the type of the biological matrices, some of them  may have the ability to  chemically interact with the analytes or  disturb the pyrolysis kinetics, thus  leading to  an incomplete degradation of the samples, which may induce suppressed or higher peak intensities.  Additionally, some biological matrices could lead to a residue buildup in the pyrolyzer  leading to a reduced sensitivity, or to some  maintenance requirements.  In order to try and reduce the impact of biological matrices on the pyrolysis results some well established cleanup steps are often necessary. These procedures  have to be carefully chosen in order to avoid destroying or altering  the samples. For this purpose, a minimal sample processing that is able to preserves the  structure of the samples while removing the possible major major interferences is required. 

Any biological tissue should require digestion and purification of extracts.  While acid and alkali digestion are routinely used currently, there is a need to develop more purification methods.  Furthermore, internal standards should be included in these steps to quantify recoveries of analytes and matrix effects.    

There are multiple steps which can help "clean up" or "remove" matrices for pyrolysis. 1. digestion, breaking down macromolecules into smaller molecules. 2. separation of particles from soluble smaller molecules through rinsing and filtration. 3. Double shot approach from pyrolysis technique, first shot at 300 C to remove volatiles, and use second shot to do pyrolysis analysis.  

The paper does a good job outlining much of this. To reiterate some of it, components in tissues can interfere with marker compounds and selected ions of those marker compounds by py-GCMS, so it's important to inspect pyrograms of those pure components to assess co-elution, production of the selected marker compounds, or ion production that interferes with the selected ions of the selected marker compounds. If there's interference from those matrix components, then cleanup steps must be used to eliminate or minimize them. The cleanup steps will depend on the tissue component materials - are they protein, mineral, carbohydrates, lipids, etc.  For example, hot water is great at washing away lipids, but would do nothing to cleanup mineral or proteins.

Complex biological matrices can greatly impact Pyr-GC/MS analysis as tissues containing lipids, proteins and other organic compounds will degrade to small molecules, hydrocarbons, ketones, aromatic compounds for example, which can overlay with compounds from the polymers. 
To reduce the interferences, tissues can be digested and polymers separated before the analysis.