Voodoo,
if FDA methods do not specify QC activity, then you might be able to define your own activity schedules. I'm not familiar with 17025, so I can't say if it also has a preferred schedule of QC activity, or just wants you to establish and maintain one.
Here is what I see, coming from the metals industry and working in a QC lab under a 9001:2008 cert: ASTM 305 for spectroscopic analysis calibration curves has section 8.2.3 on establishing frequency of verification of the calibration curves with a reference material. ASTM 882 addresses QC and accountability in the chem lab, noting the use of QC samples. CH 1 in the EPA methods is devoted to QC of analysis. This includes the method validation/verification upon instituting any method in a lab, but also covers ongoing verification activity of the method (from sampling to sample prep to actual instrument/wet analysis) as it is used down the weeks, months, and years. This includes use of matrix blank samples to watch for contamination, spiked analyte samples, and reference materials and/or matrix-matched QC samples built from individual RM's. Just some examples.
Frequency of QC: ASTM has you look at repeatability on reference materials to determine frequency of QC checks. I believe EPA has the user doing it with each batch of samples run with a method. I do metals analysis with WD-XRF and ICP-OES, and have different strategies for each. With XRF, precision is very tight and instrumental drift is not normally a big problem, so daily QC is fine for my situation. With ICP, QC depends on batch size, for me. I tend to run a QC sample, then run 5 unknowns, then run the QC again. With wet analysis for metals, I typically have a QC sample run in duplicate alongside each batch of duplicate unknowns. For physical tests, like particle size in sieves, or Ash content in coals, QC is mainly a physical calibration check of the apparatus, with maybe a yearly QC sample run to verify. It really depends on the test method and apparatus.
I'm not sure, under maintenance activity, what "IQ/OQ/PQ" meant in your post. What is calibration activity mean for you, with wet and spectrochemical analysis? Regular drift correction, or calibration by checking with a reference material?
Again, I don't know 17025, so I don't know of any constraints it imposes on frequency of QC. I AM surprised FDA methods don't go beyond initial method validation/verification specifications though. But I have no experience at all with pharma or FDA. In absence of any FDA or 17025 mandates on QC frequency, I would experiment with each piece of analytical equipment and method, to see what frequency is justified. If your methods on the spectrometers and the chromo are similar enough to each other, for each piece of equipment, then look solely at the instruments, and not by each method. Pick one method on one instrument and start with more frequent QC and watch your repeatability and accuracy. Then back off frequency until your repeatability suffers enough that you would not be comfortable with the results; say 2 sigma of the "true" value of the selected analyte in a reference material. If FDA or 17025 does not specify, you don't want to QC too much and waste time and resources running QC with each sample, when running a QC per batch of samples would suffice to show stable, repeatable analysis that one would have confidence in.
All the things you do now ARE part of QC in a lab. But in many situations, I would want to see historical evidence (trend analysis) that lab testing is able to put out quality data that is defensible. If you have to perform major maintenance on your ICP, say a new detector, how do you know the method will still be valid?
I agree with your assessor, to start in light with your scope and not try to have everything you do put under the scope of your cert, at first. One of the 3rd party labs I use did the same thing, over 10 years ago. Like you, they did myriads of different testing types, working with metals, coal, and brick. It worked out well for them.