news
RESEARCH PROFILES
Profiling the plasma proteome with IMS/MS
2D LC coupled with IMS/MS can be completed in ~3.3 h, which is ~10× less In the future, physicians may screen time than is required for conventional patients’ blood samples for hundreds of LC/MS/MS. Because IMS separation diseases by measuring levels of specific time is on the millisecond scale and proteins in plasma. Once a disease is diTOFMS has a microsecond separation agnosed, doctors may use the patient’s time, hundreds of mass spectra can unique plasma profile to optimize the be collected from one IMS spectrum. therapeutic response. But first, a Rapid analysis is important method must be developed for the because plasma samples from high-throughput detection and hundreds of healthy individuals 1200 quantification of the plethora of must be analyzed to establish the proteins in human plasma. David “normal” plasma profile, and the 1000 Clemmer, Stephen Valentine, and procedure must be repeated for 800 colleagues at Indiana University, each disease state. Predictive Physiology and MediClemmer and colleagues 600 cine, the Boston University School showed that LC/IMS/MS de400 of Medicine, the Massachusetts creased spectral congestion, 11 6 9 ) Institute of Technology, and allowing the identification of Rete 10 14 7 e (ms ntio 5 m i the Pacific Northwest National low-abundance proteins, such t n tim 18 ft 3 e (m Dri Laboratory have developed such as interleukin-21, that would be in) a method. In this issue of JPR (pp nearly impossible to isolate in the 2977–2984), they describe the absence of IMS. In all, 438 unique Plasma proteome map. The 6000 most intense feause of ion mobility spectrometry proteins from plasma were identitures from each of 10 SCX fractions are resolved in 3D by (IMS)/MS to probe the plasma fied with high confidence. The LC/IMS/MS. proteome. researchers compared these Many investigators have atproteins with a high-confidence tempted to use conventional MS apmass spectrometer, where they were plasma profile compiled from MS/MS proaches to characterize the plasma separated by m/z. By modulating the data of 18 different laboratories by the proteome. However, their efforts have field strength as ions exited the drift HUPO Plasma Proteome Project (PPP). been stymied by the multitude of diftube, the researchers could either leave Of the 889 proteins assigned by PPP, ferent proteins in plasma, as well as the the peptide ions intact or fragment 127 overlapped with those identified by fact that concentrations of proteins can them before they entered the mass Clemmer and colleagues. vary by more than a billion-fold. spectrometer. Importantly, spectra of Although the number of plasma proAccording to Clemmer, “The problem fragmented ions could be correlated teins identified by LC/IMS/MS in a relawith conventional MS approaches for with those of precursor ions. This tively short period of time is impressive, plasma profiling is that they either zero method, developed by Valentine and it’s likely just the tip of the plasma-proin on only a few proteins or they take Clemmer, allows the collision-induced teome iceberg. LC/IMS/MS is a vast ima very long time to complete.” In 1998, dissociation (CID) of peptide ions to provement over earlier methodologies, Clemmer and colleagues combined be analyzed in a single experiment, as but the technique must be optimized IMS/MS with TOFMS in a single instruopposed to the sequential selection of before the goal of clinical plasma profilment, increasing the resolution and precursor ions by conventional tandem ing is realized. According to Valentine, decreasing the analysis time of complex MS. Clemmer says, “What we have is a “One of the biggest improvements I’ve protein mixtures (Anal. Chem. 1998, 70, high-dimensionality analysis of a very looked at is in the resolution of IMS/MS. 2236–2242). In their recent study, the complicated mixture. This allows us to When you improve the resolution, you researchers applied this technology to isolate and detect small signals in the also improve the quality of the CID the analysis of the plasma proteome. presence of large signals.” spectra for protein database searches, Tryptic peptides from pooled plasma In addition to increased resolution, and that helps you make more assignsamples were fractionated by a strongLC/IMS/MS operates at lightning speed ments.” Expanded informatics capacation exchange (SCX) column and compared with conventional LC/MS/ bilities, enhanced reproducibility, and then separated by reversed-phase LC. MS approaches because of its ability further reduction of analysis time are For IMS/MS, fractionated peptides to combine IMS, CID, and TOFMS in a additional improvements to IMS/MS were ionized by ESI and pulsed into single machine. For example, a single being investigated by the researchers. a drift tube containing helium gas. plasma profiling experiment that uses —Laura Tomky Cassiday m/z
Under the influence of an electric field, ions migrated through the drift tube. There, they were separated on the basis of cross-sectional area, with more compact conformations traversing faster than more extended ones. When peptide ions reached the end of the drift tube, they entered the TOF
2884 Journal of Proteome Research • Vol. 5, No. 11, 2006
© 2006 American Chemical Society
