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Review
. 2007 Aug;107(8):3621-53.
doi: 10.1021/cr068288j. Epub 2007 Jul 25.

Accurate mass measurements in proteomics

Tao Liu  1 , Mikhail E Belov, Navdeep Jaitly, Wei-Jun Qian, Richard D Smith
Affiliations
Review

Accurate mass measurements in proteomics

Tao Liu et al. Chem Rev. 2007 Aug.
No abstract available

PubMed Disclaimer

Figures

Figure 1
Figure 1
Observed frequency as a function of ion intensity for substance P measured over 109 laser shots on a 4.7-T FTICR instrument. (a) Ions captured with gated trapping (R2 = 0.73). (b) ions captured with gated trapping and collisional cooling with a pulsed buffer gas show improved linearity due to damping of the trapping motion (R2 = 0.9). (c) Addition of quadrupolar excitation to the experimental sequence creates uniform pre-excitation conditions and provides the highest linearity in frequency versus intensity for MALDI-generated ions (R2 = 0.99). (Reprinted with permission from Reference 109. Copyright 1999 American Chemical Society.)
Figure 2
Figure 2
Distributions of mass errors with applied Gaussian function for internally and externally calibrated data for (a) MALDI measurements and (b) NanoLC-microESI measurements on a 7-T FTICR instrument. Mass errors were calculated from all spectra obtained with (a) 1.5-50 fmol of analyte and (b) 1-50 fmol of analyte. (Reprinted with permission from Reference 127. Copyright 2003 Elsevier.)
Figure 3
Figure 3
Distribution of error values observed between +10 and −10 ppm for the data of complex polypeptide mixture resulting from tryptic digestion of bovine serum albumin. Dotted line represents the interpolation curve for the experimental error distribution, while solid line shows the best fit for the experimental data with Gaussian distribution. The large majority of error values fall near zero and the distribution of error values closely resembles that of a normal error distribution with a standard deviation of 1 ppm. (Reprinted with permission from Reference 137. Copyright 1999 American Chemical Society.)
Figure 4
Figure 4
Mass accuracy histograms obtained for a Neurospora crassa fungus sample using an 11-T LC-FTICR MS. Results for instrument calibration (gray) and after recalibration (black). The number of calibration regions for TIC, m/z and peak intensity is 10×2×10=200. The systematic mass measurement error (i.e. histogram maximum position) is corrected from 5 ppm to 0 ppm and the mass error spread is improved from 3.9 to 0.8 ppm. The histogram maximum is increased > 3 times, signifying a corresponding improvement in the certainty of identifications. (Reprinted with permission from Reference 138. Copyright 2006 American Chemical Society.)
Figure 5
Figure 5
Mass errors plotted for different m/z as a function of AGC target value N with the mass peak of MRFA peptide (m/z = 524.2649) used as an internal calibrant at R = 30000: (a) m/z = 195.0876, (b) m/z = 1421.9778, and (c) m/z = 1721.9587. (Reprinted with permission from Reference 152. Copyright 2006 American Chemical Society.)
Figure 6
Figure 6
(A) A plot of the variation in the flight time (expressed as part per million) of analyte ions taken from a single sample spot. (B) A plot of the variation in the flight time (expressed as ppm) of analyte ions taken from six different sample spots. (Adapted with permission from Reference 175. Copyright 1996 Elsevier.)
Figure 7
Figure 7
Calculated isotopic pattern for the peptide MPCTEDYLSLILNR from BSA (residues 445-458) (A) without and (B) with the dibromoacetanilide mass defect label. MALDI-FTICR spectrum obtained of a BSA digest is shown in (C). Mass defect labeled-peptides are denoted with a box. Inset shows a mass scale expansion of the peaks near m/z 1957, identified as the peptide MPCTEDYLSLILNR, whose predicted isotope pattern is shown in (B). (Adapted with permission from Reference 216. Copyright 2006 American Chemical Society.)
Figure 8
Figure 8
Effects of mass deviation as a filter for removing false-positive identifications. Correct tryptic phosphopeptide identifications distribute within an 8 ppm window and an Xcorr>1.4 (boxed). False-positive identifications distribute evenly throughout the entire 50 ppm window. (Modified with permission from Reference 306. Copyright 2006 Macmillan Publishers Ltd.)
Figure 9
Figure 9
Calculated percent unique tryptic fragments (potential accurate mass tags) as a function of tryptic fragment mass at four different levels of mass measurement accuracy for the predicted proteins of yeast (A) and C. elegans (B). (Reprinted with permission from Reference 51. Copyright 2000 American Chemical Society.)
Figure 10
Figure 10
Experimental steps involved in establishing and using an AMT tag. (A) Tryptic digest of a protein mixture are analyzed by LC-MS/MS. (B) A tryptic peptide EC*C*DKPLLEK (C* represents alkylated cysteine residues) is identified by MS/MS. The calculated mass of this peptide based on its sequence (i.e. 1290.5948 Da) and its normalized elution time (NET) are then used to define this peptide in the AMT tag database. (C) In the second stage, sample is analyzed under the same LC conditions using a FTICR mass spectrometer. (D) The accurate mass (i.e. 1290.5948 Da) and NET observed for a doubly charged peptide are used to match to those of the AMT tags in the database, which leads to its confident identification (EC*C*DKPLLEK). Peptides in isotopically labeled (e.g., 18O labeling) samples can be quantified using the maximum intensities of paired monoisotopic peaks (inset).
Figure 11
Figure 11
Mass error histograms of features detected from a single LC-FTICR dataset of a human plasma sample that matched to a human plasma AMT tag database using different levels of normalized elution time (NET) constraints. The LC separation time is normalized to a 0-1 scale in NET.
Figure 12
Figure 12
Zero charge state spectra of the E. coli phosphotransferase system phosphocarrier protein HPr (Mr =9119.4 Da) detected during on-line CIEF/FTICR analysis from E. coli grown in minimal medium combined with cells grown in minimal medium containing 0.1 mg/ml of (A) Ile-D10, (B) Phe-D8, (C) Arg-13C6, (D) His-13C6 or (E) Lys-13C6. (Reprinted with permission from Reference 371. Copyright 2002 John Wiley & Sons, Ltd.)
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