What are the best protein color markers for sds-page and western transfer? I work with proteins ranging from 30-110 kd.

I suggest non colored markers for best accuracy. Use Mark12 by invitrogen

I would suggest the non-colored. You can do Ponseau staining after transfer to mark the sizes of the bands.

As for the brand, I prefer the wide-range marker from Promega. It has easily disctinguishable bands ranging from 15 kDa to 225 kDa, and it worked better for me than Invitrogen's markers. The latter are just too busy and it can be hard to figure out the exact size of the marker band, especially when you're trying to differenciate betwen 70-80-90 kDa.

i have used the amersham that big e suggested, however, the kaliedoscope precision plus from bio-rad seems to be a better alternative, both in terms of cost, and in quality and reliability. also the color will be visible even after stripping the blots, and is much brighter to begin with. i have done many regressions with bio-rad kaliedoscope markers and they are usually spot on with r2 of .98 or higher...so i don't think that the accuracy of the colors is a problem.

I agree with the suggestion tu use kaleidoscope from Bio-Rad. Noncolored markers are suppossed to be more accurate, but do not allow you to follow the course of the electrophoresis, and this can be important, as on occassions the front dye may wash out but the proteins get delayed from some reason, and you only realize after transferring or irreversibly staining the gel. I too have done regressions with the Bio-Rad markers and the accuracy seems to be better than for other brands.

I've learned to like the Invitrogen Magic-Mark standards, which develop when you add a secondary antibody (anti-IgG-HRP of various species). This way you get your markers directly on the film, and don't have to worry about trying to trace them from the blot.

As for accuracy, I'm not convinced that it matters as long as the results are reproducible. SDS-PAGE mobility is influenced by a number of different things (glycosylation, charge distribution, etc.) besides just the base molecular weight.

PAGE markers are largely relative comparisions. However, I have noticed a distinct difference between prestained and non-stained markers from two companies (Amersham and Fermentas) run side by side, which is not explained bythe companies claimed differences (typically ~1-2kDa) between the two classes of markers. However, as long as your band of interest is at the same relative position to marker, it is fine (across a narrow range of sizes rather than an exact size) - and you can use a series of different percent gels to accurately determine size by PAGE (see the posting in the Analytical chem section).

Definitely go with the unstained markers. The bands will be much sharper and more accurate, they stain nicely with any protein stain, and you can follow the migration by simply watching the dye front. You can also generally see the unstained bands during migration if you look closely, because they refract the light differently.