SOUTH BEND, Ind. -- The end result, which is all that matters, looked dishearteningly similar for Michigan State.

Stop me if you'd heard it before: an impressive (yet takeaway-less) defensive performance wasted, a smattering of special-teams shortcomings, an offense unable to finish drives, catch enough passes or make enough clutch plays ... and a few points shy of a momentum-building win. Michigan State lost five Big Ten games by a total of 13 points last season, failing to make up the inches coach Mark Dantonio often talks about, the ones separating wins and losses.

It would be easy to file Saturday's 17-13 loss to No. 22 Notre Dame with last year's near misses. The Spartans couldn't quite overcome the Irish, some trigger-happy officials (more on them later) and, ultimately, themselves.

The outcome looked familiar, but it didn't feel that way.

"It does not feel the same," Dantonio said. "I don't know how it feels. You lose a close game, it's tough. Last year against Notre Dame, I felt like we were completely outplayed [in a 20-3 loss]. ... I felt like this time, we were [in the game] right down to the end."

The Spartans were more than in the game. They outperformed Notre Dame in several areas, finishing with more first downs (19-14) and more yards (254-224). A one-dimensional Notre Dame offense entered the red zone just once in the second half.

But the Fighting Irish held the edge in the only category that matters.

"Obviously Notre Dame won the game," Dantonio said, "so you have to say they outplayed us."

Michigan State's toughest opponent Saturday, other than the Big Ten officiating crew, was itself. The Spartans had four possessions reach the red zone but emerged with only 13 points. Kevin Muma hooked a 30-yard field-goal attempt on MSU's first series. After reaching the Irish 14-yard line early in the fourth quarter, Michigan State went backwards, losing five yards on a rush and another five on a false start penalty.

MSU's most painful SIW -- that's self-inflicted wound, for the coaching cliche-challenged -- came late in the third quarter, at a time when the offense seemed to have a rhythm, especially on the ground. Facing first-and-10 from its own 47-yard line with the game tied at 10-10, Michigan State went razzle dazzle, putting the ball in the hands of true freshman receiver R.J. Shelton, who threw deep downfield into double coverage. Irish safety Matthias Farley made the easy interception.

The Spartans lost possession -- and momentum.

No, Michigan offensive coordinator Al Borges didn't hack into Michigan State's playbook. The call actually came from Dantonio, who has a defensive background but has summoned some memorable trick plays in the past, including the "Little Giants" fake field goal to beat Notre Dame in 2010.

"We had a little bit of rhythm, but I also thought we needed a big play," Dantonio told ESPN.com. "We needed to be able to go down the field, which we had not been able to do. They were overplaying RJ because he's run some jet sweeps in the first three games. I thought it was the right time."

Michigan State fans will question the decision, but they have far more questions for the officials, who called 10 penalties on the Spartans, including four pass interference penalties and defensive holding.

Three of the fouls extended drives that led to Notre Dame touchdowns. One nullified a Darqueze Dennard interception. None of the P.I. penalties was an obvious mauling. Spartans defenders weren't out of position.

Dantonio didn't directly criticize the officials but defended the defensive backs' technique -- "We played the ball the way we teach them to play the ball," he said -- and their right to go after the ball.

Asked if he had ever seen so many P.I. calls, Dantonio said. "No, never. I guess that's why we should stop talking about it right there."

Notre Dame repeatedly challenged Michigan State with back-shoulder throws. Irish coach Brian Kelly felt if they weren't completed, a flag likely would fly.

"We'll continue to do what we do," Dennard said, "basically press, man up, and we do what we do."

Spartans defensive tackle Tyler Hoover admitted the penalties were tough to handle, but maintained that, "You've got to make plays. It's not the refs. It's going to be us, all the time."

Other than forcing turnovers, Michigan State's nationally ranked defense did enough. Three times, it forced Notre Dame punts in the fourth quarter, giving the offense a chance to drive for the game-winning touchdown.

The offense had a total of one first down and 20 net yards on those possessions. But the earlier drives, the ones that went deep into Notre Dame territory, stung more.

"We've got to score touchdowns," quarterback Connor Cook said. "It's the name of the game."

Cook was pulled for the game's final possession in favor of senior Andrew Maxwell, who threw three incomplete passes before trying to scramble on fourth-and-20. Although Cook had taken a hit to his shoulder, the injury didn't play a role in the decision.

"I was a little disappointed," Cook said. "They said I was a little inaccurate, but I would have wished that the coaches had faith in me to keep me in there in a critical situation like that."

Quarterbacks coach Brad Salem told Cook afterward that Cook remains the No. 1 signal caller. Dantonio was noncommittal.

"That's something we'll have to answer at a later date," he told ESPN.com. "The only thing I can tell you is you better do something with the football. At some point in time, 13's not enough."

Michigan State has two weeks to sort out its quarterback situation, two weeks to build on a surprisingly solid rushing performance, two weeks to clean up the kicking game and find ways to complement suffocating defense with takeaways after recording eight in the first three games. The Spartans can be a dangerous team in a wide-open Big Ten, especially without Ohio State or Wisconsin on their schedule.

Dantonio and his players were proud of Saturday's performance, despite the result. And it could be a springboard.

"All our goals are still in front of us," Dennard said. "We still can go to Indy for the Big Ten championship game."

Michigan State will have to get past Michigan, Nebraska, Northwestern and the rest of a formidable Legends division to reach Naptown.

Its biggest obstacle is still itself.