Marcano and Lawson were obvious adds, as two of the Padres' top 10 prospects according to MLB Pipeline. Marcano projects as a big league middle-infield piece. Lawson underwent Tommy John surgery in March but has the upside to factor into the team's future rotation mix.
Thompson's inclusion was a bit more surprising. He owns a 5.08 ERA in 44 Minor League appearances. But the 22-year-old righty has big-time stuff, and the Padres clearly felt another team might take a gamble on Thompson as a reliever.
The most noteworthy Padres prospect left unprotected was 20-year-old outfielder Tirso Ornelas, who hasn't quite tapped into his high ceiling in the Padres farm system. But Ornelas raked in the Mexican Pacific League before sustaining a broken bone in his left arm earlier this week. And he boasts a power/on-base combo that could make him an appealing option for other teams in next month's Rule 5 Draft.
Any eligible player left unprotected can be selected by a rival club but must remain in the Majors for the duration of the season or be offered back to the Padres. Along with Ornelas (No. 17), five of the Padres' other Top 30 Prospects were left unprotected: second baseman Esteury Ruiz (No. 19), right-hander Lake Bachar (No. 23), right-hander Pedro Avila (No. 26), infielder Eguy Rosario (No. 28) and shortstop Jordy Barley (No. 29).
As for Perdomo, his Padres tenure bookends a five-years-long roster construction process. When their primary focus was young talent acquisition by any means possible, the Padres acquired Perdomo from the Rockies after Colorado selected him in the 2015 edition of the Rule 5 Draft.
At the same time Perdomo was breaking into the big leagues, San Diego spent lavishly on international prospects, made a number of shrewd trades and capitalized in the Draft. In a twist of irony, when those players finally needed to be added to the 40-man roster, it was Perdomo who gave way.
In five seasons with the Padres, Perdomo posted a 5.19 ERA, often showing flashes of becoming a useful long-relief weapon but never quite sustaining it.