Valentino Rossi said his continuing shoulder problem was the primary reason why he only qualified ninth for his first grand prix with Ducati in Qatar this weekend.
Although the Italian has not yet shown frontrunning pace for his new team, he got into the top six in practice.
Rossi said that the bike's performance was encouraging in qualifying, but that by the end of the session pain from his shoulder - which underwent surgery over the winter following a Motocross accident earlier in 2010 - was preventing him from pushing to the maximum.
"I think that without my shoulder problem, which is causing us to lose five or six tenths, we could have been on the second row today, because we were able to improve the set-up by making changes that will also be important in the foreseeable future," he said.
"Today I was able to ride the GP11 better, but by the time we used the soft tyre at the end of the session, my strength was gone. When I tried to do my lap time, there were some parts of the track where I just couldn't push.
"Anyway, we got an okay time and we still have some things we can try in the warm-up."
He believes only Casey Stoner and Dani Pedrosa's Hondas are out of reach for the Ducati - but admitted his shoulder might decide his race form as well.
"I think that as long as my shoulder lasts, we'll be able to have a pace that's relatively competitive, apart from the two Hondas," Rossi said.
"We'll see how it goes from a physical point of view in the second half of the race, after 11 or 12 laps in a row riding on the limit."
Rossi's team-mate Nicky Hayden was an unhappy 13th on the other Ducati.
"It was pretty much the same way that it has been all weekend. I just clearly wasn't fast enough," he said.
"We tried something toward the start of the session that was very similar to last year's set-up, but it didn't work. I got back on my other bike and had one decent lap going, but I made a mistake in the last corner.
"We've known since the tests in Malaysia that everybody has made a big step. It's been a frustrating weekend, and it won't be easy tomorrow starting from way back, but we're not ready to go home yet."