Is 98% purity actually good or should I be worried — need advice

Answering the narrow version, because the broad one does not have a single answer. The provenance questions are more useful than the numbers. Does the report name the batch on your vial. Is the date consistent with when that batch existed. Is it addressed to the vendor or to the person who paid for the test. Was the sample taken from general stock or supplied by the vendor. A perfect certificate for a different batch is worth nothing, and vendor-supplied samples are the most common way a genuine report ends up misleading.

Dr.GastroMayo said:

The provenance questions are more useful than the numbers.

Agreed, and mass spec answers a question purity does not: identity. High purity tells you one thing dominates the chromatogram, not that it is the molecule you ordered. A mass within about a dalton of expected is the identity check.

Dr.PulmRoch said:

Two reports on the same product from two laboratories, four percentage points apart, and no method stated on either.

Same position here, arrived at the long way round. Inter-laboratory variation comes from real methodological differences, not sloppiness: which reference standard was used and how it was itself calibrated, the gradient and column, the detection wavelength, and where the integration baseline was drawn. A percentage point or two between competent labs is expected. What is not expected is a large gap, and the usual explanation there is that one report is not of the batch in your hand.

If somebody has the primary source to hand I would rather cite it than paraphrase it.

Clinical perspective, offered as context rather than as advice.

HPLC results interpretation for certificates of analysis: when you get your Janoshik report back, here's what the numbers mean:

• Purity %: Should be >97%. Below 95% is concerning.
• Retention time: Should match reference standard for the peptide
• Related substances: Degradation products should be <2% total
• Single impurity: No individual impurity should exceed 1%

My last batch: 99.6% purity, 0.0% total related substances. Clean chromatogram with single sharp peak at expected retention time. Exactly what you want to see.