An ABRF Snapshot: ABRF 2003 Survey

1. An ABRF Snapshot: ABRF 2003 Survey Janice L. Bleibaum1, Charles Nicolet2, Gautam Sarath3, Jack Simpson4, Satya Yadav5 and Mary Young6 1Roche Palo Alto, Palo Alto, CA, 2University of Wisconsin, Madison, WI, 3USDA-ARS, Lincoln, NE, 4SAIC-Frederick, Frederick, MD, 5Cleveland Clinic Foundation, Cleveland OH, 6City of Hope, Duarte, CA

2. Abstract Technologies in use in core facilities are in flux. As new technologies are adopted, old ones are used less frequently or abandoned altogether. The ABRF Survey Research Group designed the ABRF 2003 Survey to examine technologies currently in use in core facilities as well as sample frequency and sample turnover. Technologies surveyed were categorized into four groups: mass spectrometry services, protein and peptide services, DNA services, and bioinformatics services. Respondents were also asked to describe other characteristics of their facility, including type of core facility (academic, industry, etc.), staffing levels, and funding sources. Preliminary results show strong trends in usage of specific technologies. For facilities offering mass spectrometry services, MALDI-TOF MS is the most common technology used. DNA sequencing and fragment analysis is primarily being carried out on capillary instruments; some labs still use gels. N-terminal sequencing and protein digestion are offered much more frequently than peptide synthesis or amino acid analysis. The most common bioinformatics service offered is database searching. The majority of the respondents are working in academic institutions; most core facilities are small labs of 2 to 3 scientists with a ratio of Ph.D. level scientists to B.S./M.S. scientists of 1:2.5. Funding for new instruments and new hires is often difficult, however facility support in the future is generally seen as positive. The data collected from this survey show that core facilities are important contributors to scientific research and that new technologies are adopted and utilized by core labs.

3. Introduction The ABRF was created as an organization to serve core facilities; these core facilities have offered a variety of technologies and services over the years since the beginning of ABRF. Some of these technologies are still in use but have been partially or fully superseded by newer approaches. N-terminal protein sequencing, for example, is still in use but many labs are using mass spectrometry approaches as well to obtain protein sequence. In contrast, DNA sequencing has expanded as more labs are using capillary versus gel-based sequencers. The ABRF Survey Research Group designed the ABRF 2003 Survey to get a snapshot of technologies and/or services offered by core facilities. The last time the ABRF was surveyed on this topic was in 1998. Newer data gleaned from this survey will allow us to track trends in core facility technologies. The survey also included questions regarding staff composition and funding issues. The purpose of these questions was to discover how facilities are managing financially and to determine how funding may be affecting the adoption of new technologies.

4. Materials and Methods The ABRF 2003 Survey was a completely web-based survey. Members and non-members were notified of the survey through e-mail announcements. The announcements included a login name and password that respondents needed to access the survey at the ABRF web site. A password was used so that random web surfers would not be able to complete the survey. The survey was open for approximately one month. We received 95 responses; however not all respondents answered every question. The data collected was accessible as a tab-delimited file from the web site to committee members. This file was easily converted into an Excel spreadsheet. For each technology, we have graphed the percentage of total responses, mean samples per month, and mean turnaround time. Ranges varied widely and this sometimes necessitated the use of a logarithmic scale. For the sake of simplicity, some technologies and comments were excluded from the graphs but these will be included in a future publication. For questions querying the composition of core facilities, we have graphed the educational level of core facility staff as well as the mean number of staff for each type of facility (academic, industry, government, etc.). In addition, we have graphed the cost recovery from user fees for three types of core facilities: academic, research institutes, and government labs.

13. Cost Recovery From User Fees Percentage of laboratories that rely on: 100%, 50-95% or <50% cost recovery from user fees. Industrial and CRO labs not included. Industrial labs were internally subsidized and CRO labs rely exclusively on user fees.

14. Summary • Core Lab Staffing • With a few exceptions, most core labs consist of fewer than 10 scientists, • with BS/MS scientists outnumbering Ph.D.’s by ~ 4:1. • Cost Recovery • Most academic and research institutes rely heavily on user’s fees as the • main method of cost recovery. Industrial and government labs are more • routinely subsidized internally. • New Instruments and New Hires • Most laboratories can purchase new instrumentation with varying degrees • of difficultly, but essentially all laboratories surveyed have a very difficult time • obtaining approval for new hires. • Discontinued Services • Amino Acid Analysis (AAA) and oligonucleotide synthesis were mentioned • as the most frequently discontinued services.

15. DNA Technologies • • DNA sequencing is a widespread activity among survey respondents, practiced by 48.5% of those taking the survey. Capillary sequencers continue to gain in popularity at the expense of gel-based platforms. • • Microarray technologies are practiced in about as many labs as carry out oligonucleotide synthesis. • Mass Spectrometry Technologies • • MALDI-TOF is the most popular mass spectrometry technique; most MALDI-TOF samples are either peptide mass fingerprints or oligo QC samples. • • ESI-Ion Trap and ESI-QTOF instruments are both used for a variety of samples with LC-MS/MS samples predominating. • • ESI-Triple Quad instruments are still in use, but at very low levels. • Protein & Peptide Technologies • • High sample numbers/ month accompanied by short turnaround times suggest automation or a large commitment of personnel to that specific operation. • N-terminal Sequencing and many of the other services appear to be on the decline. • Lab specialization in specific techniques is increasing. • Peptide Libraries are a service barely called for. • The huge range in the number of monthly samples exhibited by labs responding to the survey indicates that the ABRF is a broad based organization serving many constituencies.

16. Acknowledgements The ABRF Survey Committee wishes to thank all who took the time to respond to this survey. Your contributions will further the mission of the ABRF. JTS acknowledges support by NCI Contract No. NO1 - CO – 12400. GS acknowledges NIH Grant Number 1 P20 RR16469 from the BRIN Program of the National Center for Research Resources.