Alex Rodriguez, the lone holdout against a suspension, faces an arbitration hearing in coming months that likely will include such evidence. The New York Yankees third baseman was suspended for 211 games from Thursday through the 2014 season, though he is allowed to play until a decision is issued by arbitrator Fredric Horowitz, which is not expected until at least November.
Until now, nearly all suspensions under MLB's drug program resulted from positive drug tests. The Biogenesis probe revealed players were using PEDs without detection.
"To catch the most sophisticated intentional fraudsters, you have to use non-analytical means, which is another reason why baseball's effort here is such a pivotal moment for the anti-doping fight," said Travis Tygart, chief executive office of the U.S. Anti-Doping Agency.
MLB officials would not speak for attribution about its investigation. The league used about 30 people full time in its fact-gathering, another person familiar with the process said Tuesday, also on condition of anonymity because no statements were authorized.
The probe was sparked in January when the Miami New Times published documents linking players to the clinic and accused it of distributing banned performance-enhancing drugs.
Technology has evolved since 2003, when federal agents raided the Bay Area Laboratory Co-Operative in Burlingame, Calif., sparking an investigation that eventually led to criminal convictions of Barry Bonds, track star Marion Jones, cyclist Tammy Thomas and NFL lineman Dana Stubblefield.
And when former Sen. George Mitchell issued his report on drugs in baseball four years later, he recommended baseball start an investigations department. Dan Mullin, a former New York City Police Officer, was hired as the unit's head in 2008. Former U.S. Secret Service director Mark Sullivan was brought in to assist in the Biogenesis probe.
After the Miami New Times report, baseball investigators examined the Facebook pages of Bosch and Porter Fisher, the former Biogenesis associate who gave documents to the newspaper. They began to sketch out which people they were friends with, and which of those friends posted photos of athletes or mentioned athletes. Each link led to new loops that provided leads.
MLB filed a lawsuit in March against Biogenesis of America, company founder Anthony Bosch and others, complaining they interfered with the contracts between MLB and the union. The suit was unusual and may never reach trial, but it did give MLB the ability to file civil subpoenas.
Records from Florida's Circuit Court for Miami-Dade County that were examined by the AP showed subpoenas were issued to Federal Express, AT&T Mobility, T-Mobile USA, UPS and Metro PCS. At least some of those companies complied and turned over data to the probe, one of the people said.
By June, Bosch agreed to co-operate with the investigation. The person said MLB hired a data recovery company to obtain records from his mobile telephone.
When baseball officials met with the union, evidence included the BlackBerry instant message transcripts and records of text messages. Lawyers for players believed some emails also had been recovered.
"It's like traditional law enforcement methods," Tygart said. "Even without the powers of law enforcement — wiretaps, search warrants — you can still have success in obtaining these documents."