How do very long chain fatty acids, cholesterol, lipids, phospholipids, etc. impact the typical polymer indicator ions used for quantifying MNPs by py-GC/MS?

I have very limited experience with pyrolysis-GC/MS, but I am aware that some lipids can degrade into hydrocarbons that may co-elute with plastic pyrolysis products. There is also the possibility of some ion overlap. My experience with other MS/MS techniques suggests that these compounds are also likely to contaminate columns, which is likely more prevalent in GC columns. 

I do not have direct experience of py-GC-MS in this field, so cannot provide informed comment.

The very long chain fatty acids, cholesterol, lipids, and phospholipids from the biological tissues can  interfere with the  quantification of  MNPs when using pyrolysis-gas chromatography/mass spectrometry. During the pyrolysis stage, these matrix components have the ability to decompose  into a range of hydrocarbon fragments, alcohols, ketones, and alkenes. These constituents could  co-elute with the polymer pyrolysates and share common ion fragments. This problem usually appear in the case of  polyethylene (PE) and polypropylene (PP), that are able to produce broad hydrocarbon pyrolysis profiles that are also produced by lipids and sterols. In this case the results can lead to false positives or to an overestimation of the plastics concentration.   Furthermore, the presence of neutral lipids, cholesterol, and phospholipids can suppress the ionization of target polymer fragments, especially in the case of complex or lipid-rich samples. This could give an underestimation of various types of  plastics, like PET or PS. Moreover, the decomposition  products obtained from  biological molecules such as phospholipids may be similar to the ones that are obtained by pyrolysis from PLA or PHB. This could increase the potential risk  of misidentifying  some natural residues as synthetic plastics.  

In case of incomplete digestions of these natural compounds, there is the possibility of formation of the indicator ions used for some polymers. PE is an example with fatty acids. The implication is an overestimation of the amount of MNP actually present in the case of insufficient digestion. It is to be noted that in such cases almost complete digestion efficiency is needed to avoid the overestimation. A way of minimizing the overestimation is the use of multiple indicator ions for the quantification of MNPs by py-GC/MS. Samples with an indication of natural compounds having affected the analytical outcomes, should be discarded.

GC-MS pyrogram of polyethylene (PE) consists of a weak α,ω-alkadiene peak followed by a dominant 1-alkene peak and a minor n-alkane peak (characteristic three peaks).  Fatty acids also show similar homologous series with varying repetitions of the triple peaks as a function of chain length (three peaks).

These substances can provide some false signals (monomer, dimer, trimer, etc) for the more aliphatic polymers such as Polyethylenes and polypropylenes. This can be minimized by extracting these organics from the matrix, either with solvent or thermally.  Also, care should be taken to select "unique" target pyrolyzates. It is tempting to use the lower MW pyrolyzates, especially when they are the strongest signal. But, it is more important to select a pyrolyzate that is unlikely to be the result of a natural polymeric material. Similar mass spectrum of natural polymer pyrolyzates can be supplementarily differentiated from its synthetic doppelganger using Retention Indices as a confirmative measure. 

I dont know.  I'd need to study their pyrograms. Even still, I can be certain that they will produce the PAH marker compounds often used to quantify PVC, so PVC is very problematic.

Most polymers use fragment ion from pyrolysis as indicator ions to represent its presence. However, the similar fragment ion could be yield by lipids listed above. For example, the C21H44 hydrocarbon fragment is used for representing PE, while any lipid with long hydrocarbon chain (>21) could generate such fragment in pyrolysis, which introduce background and lead to potential false positive identification.

Lipids and fatty acids can thermally degrade into alkenes, alkanes, and ketones. They are similar to Pyrolysis products of polyethylene and polypropylene. 
Cholesterol and Sterols can generate aromatic hydrocarbons and cyclic compounds upon pyrolysis and they are similar to pyrolysis products of polystyrene containing polymers. 
Phospholipids can degrade to phosphate-containing fragments and long-chain hydrocarbons, which can interfere with nylon, PET, and other polar polymers.