Armed with survey software, ProteoMonitor embarked on a guided tour of the protein mass spectrometry landscape last month. We conducted an e-mail survey of 2,000 readers of GenomeWeb’s proteomics and mass spec news channel and received reponses from 173 of them. The survey results have a ±7.6 percent maximum sampling error at a 95 percent confidence level. The data collected represent a measure of how users are applying mass spectrometry to protein analysis, and what they think of the tools they’re using. For a graphic presentation of the results, see p. 6-10.
An analysis of the data suggests three conclusions: that Applied Biosystems Voyager MALDI-TOFs and Thermo Finnigan LCQ Deca ion traps are currently the most popular instruments applied to protein analysis; that MALDI-TOF/TOFs are at the top of respondents’ wish lists for future purchases; and that the field of protein mass spectrometry is split equally among users who prefer buying mass spectrometers alone or as part of a package deal with protein separation equipment.
Almost half of those who answered the questionnaire hailed from academic laboratories, and about 20 percent were employed in the biotech industry. Researchers at government laboratories, pharmaceutical company laboratories, and proteomics research companies were represented equally among the remaining 30 percent.
Respondents’ titles varied to a greater extent. About 15 percent characterized themselves as mass spectrometry group leaders, another 15 percent were post-docs, and 10 percent held positions as staff scientists in mass spectrometry laboratories. But by far the largest percentage, around 30 percent, filed their title under the “other” category, which contained responses as varied as graduate student, bioinformatics analyst, and manager of proteomics resource facility.
As for how the 173 respondents applied their mass spectrometers to protein analysis applications, 119 of the respondents said they performed protein identification, 91 said they used mass spectrometry in differential proteomics experiments, 86 identified the components of protein complexes, and 76 used mass spectrometry to study post-translational modifications.
Given that almost 50 percent of the respondents worked in academic laboratories, it comes as no surprise that 50 percent cited academic research as the purpose of their proteomics research. However, another 25 percent aligned themselves with protein target discovery, and 13 percent with pharmaceutical development.
Of the factors most important to consider when purchasing a mass spectrometer, respondents placed sensitivity, reliability, accurate mass measurement, MS/MS capability, and resolution at the top of the list of 15 factors. As for least important, respondents listed laboratory footprint, throughput, automation, and overall reputation of the vendor.
When respondents listed the number and type of mass spectrometers in their labs, both the Thermo Finnigan LCQ Deca ion trap and Applied Biosystems Voyager MALDI-TOF emerged as the most popular, with totals of 51 and 46 instruments, respectively. Following behind were the ABI/MDS Sciex QSTAR Q-TOF and Kratos Axima MALDI-TOF, with 31 and 24, respectively. It should be noted that the survey did not control for multiple responses from the same lab, and so total numbers might not be accurate. None of the respondents used a Bruker Daltonics MALDI-TOF/TOF, and the survey counted a total of three ABI MALDI-TOF/TOF mass spectrometers. Three respondents used a Ciphergen ProteinChip SELDI mass spectrometry system, and one respondent reported using a homemade MALDI Q-TOF.
Of the respondents who indicated how much they had spent in the last two years on mass spectrometers, 65 percent had spent at least $100,000, and 15 percent had spent at least $1 million. That spending trend seems likely to continue, as 63 percent of the respondents who indicated they would purchase mass spectrometry equipment in the next two years said they would spend at least $100,000. Twelve percent said they were likely to spend at least $1 million in the next two years.
Thirty-four respondents said they were planning to purchase MALDI-TOF/TOF mass spectrometers within two years, according to the survey, followed closely by MALDI-TOF and Q-TOF mass spectrometers. Sixteen respondents said they were likely to purchase an electrospray ion trap mass spectrometer.
When asked which mass spectrometer they would purchase if cost were not an issue, 44 percent of the respondents indicated a MALDI-TOF/TOF would be their choice, followed by a Q-TOF, with 19 percent, and a FT/MS instrument, with 15 percent.
Lastly, survey respondents were split almost evenly on the question of whether they preferred to purchase a mass spectrometer packaged along with a compatible separations system, or whether they preferred to purchase mass spectrometers independently. Fifty-four percent favored purchasing a stand-alone instrument, compared with 46 percent who said they’d opt for a package deal.