June 30, 2017
The 2017 ABRF Workflow Interest Network (WIN) is pleased to announce initiation of Phase 2 of a study to promote inter-laboratory reproducibility of quantitative proteomic LC-MS/MS analyses. Past studies of proteomic performance metrics have focused on the retrospective evaluation of collected data. In this study we seek to identify data processing tools, including ID-free quality metrics, to support a proactive approach.
Participating laboratories will receive 2 samples: a mixture of peptide internal standards and a HeLa cell lysate digest. A detailed protocol on how to run these samples will be provided when the samples are shipped. We estimate it should take no more than 24 hours to complete the analysis. Participating laboratories will submit raw files and complete a questionnaire of self-reporting parameters according to our instructions. Results derived from the raw data will be de-identified to maintain the anonymity of the participating laboratories. Each participant will receive a unique identification number allowing them to compare their results with those of other participating laboratories.
The timeline for the study is as follows:
- Sample requests accepted until August 1, 2017
- Samples ship to participants starting August 1, 2017
- Raw data files uploaded to the online repository by October 31, 2017
- Results and analysis presented at the ABRF 2018 conference April 22-25, 2018, in Myrtle Beach, South Carolina, USA, then posted on the ABRF website.
To request a sample, please go to https://www.surveymonkey.com/r/H8XVSF3 and provide your shipping information before August 1, 2017. The WIN is eager to obtain data from a variety of different laboratories and mass spectrometry platforms, and encourages all mass spectrometry laboratories with an interest in proteomics and data quality metrics to participate. However, because sample preparation and shipping involve a significant investment of time and money, Phase 2 is limited to 40 participants. The research group asks that you only request a sample if you are confident that you will be able to provide your raw files by the end of October. We thank you for your support of the ABRF and look forward to your participation in this study.
The ABRF Workflow Interest Network
Emily Chen (chair), Achim Treumann, Alex Campos, LeeAnn Higgins, Sheng Zhang, Theresa McLaughlin, and Allis Chien (EB liaison)