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Beginning 2007, heavy-duty engine certification would require that in-use emissions from vehicles be measured under ‘real-world’ operating conditions using on-board measurement devices. An on-board portable emissions measurement system called Mobile Emissions Measurement System (MEMS) was developed at West Virginia University (WVU) to record in-use, continuous and brake-specific emissions from heavy-duty diesel-powered vehicles. The objective of this paper is to present a preliminary development of a test data quality assurance methodology for emissions measured using the any portable emissions measurement system (PEMS). The first stage of the methodology requires ensuring the proper operation of the different sensors and transducers during data collection. The second stage is data synchronization and pre-processing. The next stage is systematic checking of possible errors from transducers and sensors.