Two-dimensional separation by nano-LC and trapped ion mobility spectrometry (TIMS) prior to Q/TOF tandem mass spectrometry significantly improves the accuracy of isobaric tag-based quantitation in proteome analysis without the need for additional measurement time for TIMS insertion between LC and Q/TOF MS. The obtained peak capacity of up to 3300 h–1 in LC/TIMS reduced the coisolation of precursor ions at the quadrupole analyzer, resulting in more accurate ratios of reporter ions derived from isobaric tags in product ion spectra obtained at the TOF analyzer. We also found that TIMS with a narrower quadrupole isolation window could reduce the ratio compression effect at least as effectively as the synchronous precursor selection method using MS3 scans without compromising sensitivity or coverage. Our results suggest that the 65 min gradient LC/TIMS/Q/TOF system is an excellent platform for high-throughput proteomics studies.

The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge states. However, it is necessary to know how phosphate groups affect the peptide collision cross sections (CCS) in order to accurately predict phosphopeptide CCS values and to maximize the usefulness of IMS. In this work, we systematically characterized the CCS values of 4,433 pairs of mono-phosphopeptide and corresponding unphosphorylated peptide ions using trapped ion mobility spectrometry (TIMS). Nearly one-third of the mono-phosphopeptide ions evaluated here showed smaller CCS values than their unphosphorylated counterparts, even though phosphorylation results in a mass increase of 80 Da. Significant changes of CCS upon phosphorylation occurred mainly in structurally extended peptides with large numbers of basic groups, possibly reflecting intramolecular interactions between phosphate and basic groups.

This paper describes the first successful realization of the magnetic detection of the free boundary plasma shift for helical plasmas. A procedure for determining the equilibrium plasma displacement in a stellarator by means of external magnetic field measurements (psi loops and modulated Rogowski coils) is discussed. Recent experimental results, the normalized displacement Δb/ap as a function of volume averaged beta ⟨β⟩, are discussed and compared with analytical and published numerical MHD computational results. The typical measured plasma boundary shift, Δb/ap, in the standard Heliotron-E configuration (Rp = 2.20 m, ap = 0.21 m, ι(0)/2π ~ 0.53, ι(ap)/2π ~ 2.8) is (8-10) × 10-3, when the volume averaged beta is 0.50%. The measured normalized plasma boundary shift is nearly proportional to the diamagnetic volume averaged beta, for values of beta up to 0.95%. The magnetically determined plasma boundary shift Δb is less than 3 mm. The experimental observations on shift (Δb/ap versus ⟨β⟩dia) are compared with the analytically expected plasma boundary shift. The measured shift lies in the range between the expected upper limit (Δb/ap = β(0)/2βeq) and the lower limit (Δb/ap= ⟨β⟩/2βeq), where βeq=[ι(ap)/2π]2(ap/Rp) ~ 0.77 for the standard configuration of Heliotron-E. It is found that the measured plasma boundary shift depends strongly on the initial vacuum magnetic configuration parameters such as the horizontal position of the magnetic axis and the rotational transform. When the vacuum magnetic axis is shifted inward towards the major axis, significant decreases of the normalized plasma shift (Δb/ap) and of the plasma induced vertical field are observed, which are interpreted as being due to a reduction of the Pfirsch-Schluter current

The contribution of peptide amino acid sequence to collision cross section values (CCS) has been investigated using a dataset of ∼134 000 peptides of four different charge states (1+ to 4+). The migration data were acquired using a two-dimensional liquid chromatography (LC)/trapped ion mobility spectrometry/quadrupole/time-of-flight mass spectrometry (MS) analysis of HeLa cell digests created using seven different proteases and was converted to CCS values. Following the previously reported modeling approaches using intrinsic size parameters (ISP), we extended this methodology to encode the position of individual residues within a peptide sequence. A generalized prediction model was built by dividing the dataset into eight groups (four charges for both tryptic/nontryptic peptides). Position-dependent ISPs were independently optimized for the eight subsets of peptides, resulting in prediction accuracy of ∼0.981 for the entire population of peptides. We find that ion mobility is strongly affected by the peptide’s ability to solvate the positively charged sites. Internal positioning of polar residues and proline leads to decreased CCS values as they improve charge solvation; conversely, this ability decreases with increasing peptide charge due to electrostatic repulsion. Furthermore, higher helical propensity and peptide hydrophobicity result in a preferential formation of extended structures with higher than predicted CCS values. Finally, acidic/basic residues exhibit position-dependent ISP behavior consistent with electrostatic interaction with the peptide macrodipole, which affects the peptide helicity. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository () with the dataset identifiers PXD021440/JPST000959, PXD022800/JPST001017, and PXD026087/ JPST001176.