How to negotiate with collaborators on adjusting procedures to interdisciplinary projects? This is an issue I frequently face. As a biologist I like doing interdisciplinary science. In fact I believe interdisciplinarity is the key to producing any truly insightful observation, at least in my field of work. 
Typically I deal with arthropod morphology, allied to some biochemistry, with some conclusions relevant for general biology, ecology, evolution. Since recently I've added some molecular biology (i.e. DNA analyses) to this. 

Now my problem is that my main expertise lies in morphology and natural history – because I have seen and read a lot on my bugs. But because of my interdisciplinary approach, I have some insights into what’s happening around. I just don’t know their protocols, don’t have their reagents, lack the experience and background know-how to plan and analyse their results.

However frequently I run into (minor) conflicts over interpreting their results in face of the bigger picture. Usually they get upset when I come up with a different final conclusion, and instead of trying to logically convince me, they get all evasive repeating I am not qualified enough to discuss their work.

It will try to illustrate some typical situations:


A group of collaborators do some proteomic analysis of an organ, and come up with exciting compounds therein reported for the first time. But I do not understand why, out of a 15-lines-long list of potential candidates, the most exciting one is surely the correct identification. (I do have superficial understanding of database identification scores, but likely not as much as they [must] have, and would be delighted to learn more).
Some skilful biochemist isolates a compound as I suggested and starts on further bioassays but while using solvents and plastic labware. From my general experience around GC-MS machines and organic solvents, there will be an uncontrolled amount of phthalate esters released in the extracts which may account for significant effects. Even when alerted of this problem prior to procedures, plastic and solvents are used because “this is how we do it”. Some guy protested “ethanol isn’t exactly a solvent” when shutting his ears and going all offended.
A chemist will use antibiotics solutions which did not really solubilise, categorically stating “suspensions of medicines work”.


There are countless such cases. I try as best to be always prepared to receive their questions and skepticism around my own specialities as I feel confident enough to explain the rationale. And alas, they may be seeing something I did not. However I feel almost everyone else is unwilling to discuss and question routine protocols, and this makes doing interdisciplinary science very hard!

How can I avoid such conflicts, adjust procedures, and at the same time reach an agreement with collaborators?
It seems to me that the problem lies on a psychological aspect of their lives and your way of questioning is triggering this response on them. Maybe they're insecure about their academic formation or have been challenged in the past in a way that made them develop a very defensive stance when questioned. My suggestion is that you change your way of obtaining this info to a more friendly one. usually lowering your guard creates the same behavior on others. You could go for something like "I have no knowledge about this. Could you please teach me X? I feel it's important for my formation."