Hadamard transform capillary electrophoresis

This paper reports the first demonstration of a multiplex sample injection technique in capillary electrophoresis. The sample was injected into a capillary (effective length, 4 cm) as a pseudorandam Hadamard sequence by a photodegradation technique using a high-power gating laser, and the fluorescence signal, which was measured using a probe excitation beam, was decoded by an inverse Hadamard transformation. The signal-to-noise ratio was improved by a factor of 8, which was in good agreement with the theoretically predicted value of 8.02. This approach is potentially useful for the enhancement of the sensitivity by 3 orders of magnitude in high-resolution capillary electrophoresis, combined with fluorescence detection.     

Shotgun protein sequencing by tandem mass spectra assembly

The analysis of mass spectrometry data is still largely based on identification of single MS/MS spectra and does not attempt to make use of the extra information available in multiple MS/MS spectra from partially or completely overlapping peptides. Analysis of MS/MS spectra from multiple overlapping peptides opens up the possibility of assembling MS/MS spectra into entire proteins, similarly to the assembly of overlapping DNA reads into entire genomes. In this paper, we present for the first time a way to detect, score, and interpret overlaps between uninterpreted MS/MS spectra in an attempt to sequence entire proteins rather than individual peptides. We show that this approach not only extends the length of reconstructed amino acid sequences but also dramatically improves the quality of de novo peptide sequencing, even for low mass accuracy MS/MS data.     

Hadamard transform time-of-flight mass spectrometry: a high-speed detector for capillary-format separations

This work demonstrates that with an intrinsic duty cycle of 50% and spectral storage speeds up to 277 spectra s(-1) Hadamard transform time-of-flight mass spectrometry (HT-TOFMS) is a promising detector for any capillary-format separation that can be coupled to MS by electrospray ionization. Complete resolution of the components of a nine-peptide standard was achieved by coupling pressurized-capillary electrophoresis (pCE) to HT-TOFMS. The addition of pressure to the separation capillary decreased analysis times and stabilized the electrospray ionization source. Pulsed-pressurized injection of reserpine was used to experimentally simulate narrower peaks than those obtained in the pCE. HT-TOFMS was able to sample peaks having widths in the millisecond range.     

Automatic validation of phosphopeptide identifications from tandem mass spectra

We developed and compared two approaches for automated validation of phosphopeptide tandem mass spectra identified using database searching algorithms. Phosphopeptide identifications were obtained through SEQUEST searches of a protein database appended with its decoy (reversed sequences). Statistical evaluation and iterative searches were employed to create a high-quality data set of phosphopeptides. Automation of postsearch validation was approached by two different strategies. By using statistical multiple testing, we calculate a p value for each tentative peptide phosphorylation. In a second method, we use a support vector machine (SVM; a machine learning algorithm) binary classifier to predict whether a tentative peptide phosphorylation is true. We show good agreement (85%) between postsearch validation of phosphopeptide/spectrum matches by multiple testing and that from support vector machines. Automatic methods conform very well with manual expert validation in a blinded test. Additionally, the algorithms were tested on the identification of synthetic phosphopeptides. We show that phosphate neutral losses in tandem mass spectra can be used to assess the correctness of phosphopeptide/spectrum matches. An SVM classifier with a radial basis function provided classification accuracy from 95.7% to 96.8% of the positive data set, depending on search algorithm used. Establishing the efficacy of an identification is a necessary step for further postsearch interrogation of the spectra for complete localization of phosphorylation sites. Our current implementation performs validation of phosphoserine/phosphothreonine-containing peptides having one or two phosphorylation sites from data gathered on an ion trap mass spectrometer. The SVM-based algorithm has been implemented in the software package DeBunker. We illustrate the application of the SVM-based software DeBunker on a large phosphorylation data set.     

Applications of Hadamard transform to gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry

Successful application of the Hadamard transform (HT) technique to gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/mass spectrometry (LC/MS) is described. Novel sample injection devices were developed to achieve multiple sample injections in both GC and LC instruments. Air pressure was controlled by an electromagnetic valve in GC, while a syringe pump and Tee connector were employed for the injection device in LC. Two well-known, abused drugs, 3,4-methylenedioxy-N-methylamphetamine (MDMA) and N, N-dimethyltryptamine (DMT), were employed as model samples. Both of the injection devices permitted precise successive injections, resulting in clearly modulated chromatograms encoded by Hadamard matrices. After inverse Hadamard transformation of the encoded chromatogram, the signal-to-noise (S/N) ratios of the signals were substantially improved compared with those expected from theoretical values. The S/N ratios were enhanced approximately 10-fold in HT-GC/MS and 6.8 in HT-LC/MS, using the matrices of 1023 and 511, respectively. The HT-GC/MS was successfully applied to the determination of MDMA in the urine sample of a suspect.     

Hadamard transform ion mobility spectrometry

A detection scheme that makes use of the Hadamard transform has been employed with an atmospheric-pressure ion mobility spectrometer fitted with an electrospray ionization source. The Hadamard transform was implemented through the use of a linear-feedback shift register to produce a pseudorandom sequence of 1023 points. This pseudorandom sequence was applied to the ion gate of the spectrometer, and deconvolution of the ion signal was accomplished by the Hadamard transform to reconstruct the mobility spectrum. Ion mobility spectra were collected in both a conventional and Hadamard mode, with comparisons made between the two approaches. Initial results exhibited low spectral definition, so an oversampling technique was applied to increase the number of data points across each analyte spectral peak. The use of the Hadamard transform increases the duty cycle of the instrument to 50% and results in a roughly 5-fold enhancement of the signal-to-noise ratio with a negligible loss of instrument resolution. It is also shown that any potential multiplex disadvantage, which limits the attractiveness of some high-throughput techniques, is not a limiting factor in this new implementation.     

Hadamard transform ion mobility spectrometry

Traditionally, the spectrum acquired using ion mobility spectrometry (IMS) is an average of multiple experimental cycles. Each cycle is initiated by passing a short burst of ions into a drift tube containing a homogeneous electric field. Prior to starting the subsequent cycle, all ions in the system must arrive at the detector or spectral overlap may occur. To maximize resolution, the ion pulse admitted to the drift tube is small in relation to the total scan time with the unfortunate consequence of an inherently low duty cycle (approximately 1%). Offering an improved SNR through a 50% duty cycle, the Hadamard transform (HT) applied to ion mobility spectrometry represents a fresh alternative to signal-averaged data acquisition. Initial results from measurements of amphetamine and cytochrome c samples indicate a 2-10-fold increase in SNR for the HT-IMS technique with no reduction in resolution.     

Absorption-mode: the next generation of Fourier transform mass spectra

The Fourier transform spectrum can be presented in the absorption-mode (commonly used in FT-NMR), magnitude-mode (FT-ICR), and power-mode (engineering applications). As is routinely used in FT-NMR, it is well-known that the absorption-mode display gives a much narrower peak shape which greatly improves the spectrum; recently, the successful solution of the phase equation allowed broadband phase correction which makes it possible to apply the absorption-mode routinely in FT-ICR. With the empirical evidence provided herein, it has been confirmed that in addition to the improvement on resolving power, compared to the conventional magnitude-mode, the new absorption-mode improves the signal-to-noise ratio (S/N) of a spectrum by 1.4-fold and can improve the mass accuracy up to 2-fold with no extra cost in instrumentation. Therefore, it is worthwhile to apply and promote absorption-mode in routine FT-ICR experiments.     

CIFTER: automated charge-state determination for peptide tandem mass spectra

Tandem mass spectrometry (MS/MS) has become a common and useful tool for analyzing complex protein mixtures. Database search programs are the most popular means for peptide identification from MS/MS spectra. However, estimations of charge states of peptide MS/MS spectra obtained from low-resolution mass spectrometers have not been reliable. They require repetitive database searches and additional analyses of the search results. We propose here an algorithm designed to reliably differentiate doubly charged spectra from triply charged ones. We conducted a rigorous analysis of various spectral features and their effects. We employed the distinguishing features found in our analysis and developed a classifier for multiply charged spectra using a machine learning approach. The test on various data sets showed that our method could be successfully applied independent of experimental setup and mass instrument. This algorithm can be used to prefilter spectra so that only reasonably good spectra are submitted to database search programs, thereby saving considerable time. The software for MS/MS charge-state determination, which we named "CIFTER", is available at a website http://prix.uos.ac.kr/sifter/cifter.     

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra

For automated production of tandem mass spectrometric data for proteins and peptides >3 kDa at >50 000 resolution, a dual online-offline approach is presented here that improves upon standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategies. An integrated hardware and software infrastructure analyzes online LC-MS data and intelligently determines which targets to interrogate offline using a posteriori knowledge such as prior observation, identification, and degree of characterization. This platform represents a way to implement accurate mass inclusion and exclusion lists in the context of a proteome project, automating collection of high-resolution MS/MS data that cannot currently be acquired on a chromatographic time scale at equivalent spectral quality. For intact proteins from an acid extract of human nuclei fractionated by reversed-phase liquid chromatography (RPLC), the automated offline system generated 57 successful identifications of protein forms arising from 30 distinct genes, a substantial improvement over online LC-MS/MS using the same 12 T LTQ FT Ultra instrument. Analysis of human nuclei subjected to a shotgun Lys-C digest using the same RPLC/automated offline sampling identified 147 unique peptides containing 29 co- and post-translational modifications. Expectation values ranged from 10 (-5) to 10 (-99), allowing routine multiplexed identifications.     

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

Reliable identification of posttranslational modifications is key to understanding various cellular regulatory processes. We describe a tool, InsPecT, to identify posttranslational modifications using tandem mass spectrometry data. InsPecT constructs database filters that proved to be very successful in genomics searches. Given an MS/MS spectrum S and a database D, a database filter selects a small fraction of database D that is guaranteed (with high probability) to contain a peptide that produced S. InsPecT uses peptide sequence tags as efficient filters that reduce the size of the database by a few orders of magnitude while retaining the correct peptide with very high probability. In addition to filtering, InsPecT also uses novel algorithms for scoring and validating in the presence of modifications, without explicit enumeration of all variants. InsPecT identifies modified peptides with better or equivalent accuracy than other database search tools while being 2 orders of magnitude faster than SEQUEST, and substantially faster than X!TANDEM on complex mixtures. The tool was used to identify a number of novel modifications in different data sets, including many phosphopeptides in data provided by Alliance for Cellular Signaling that were missed by other tools.     

Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra

High-resolution and high-accuracy Fourier transform mass spectrometry (FTMS) is becoming increasingly attractive due to its specificity. However, the speed of tandem FTMS analysis severely limits the competitive advantage of this approach relative to faster low-resolution quadrupole ion trap MS/MS instruments. Here we demonstrate an entirely FTMS-based analysis method with a 2.5-3.0-fold greater throughput than a conventional FT MS/MS approach. The method consists of accumulating together the MS/MS fragments ions from multiple precursors, with subsequent high-resolution analysis of the mixture. Following acquisition, the multiplexed spectrum is deconvoluted into individual MS/MS spectra which are then combined into a single concatenated file and submitted for peptide identification to a search engine. The method is tested both in silico using a database of MS/MS spectra as well as in situ using a modified LTQ Orbitrap mass spectrometer. The performance of the method in the experiment was consistent with theoretical expectations.     

Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra

We have developed an approach to identify the molecular weight of a peptide ion directly from its corresponding tandem mass spectrum using a cross-correlation function. We have shown that the monoisotopic molecular weight can be calculated for approximately 90% of tandem mass spectra identified from tryptic digests of complex protein mixtures. The accuracy of the calculated monoisotopic masses was dependent on the resolution and mass accuracy of the spectra analyzed, but was typically <0.25 amu for linear ion trap mass spectra. The ability to calculate accurate monoisotopic molecular weights for low-resolution ion trap data should significantly improve both the speed and performance of database searches for which typical mass accuracies of approximately 3 amu are employed. In addition, this strategy can also be used to identify the precursor ion for tandem mass spectra acquired using large ion selection windows in data-independent collision-activated dissociation and has the potential to identify multiplexed tandem mass spectra.     

Variation of the Fourier transform mass spectra phase function with experimental parameters

It has been known for almost 40 years that phase correction of Fourier transform ion cyclotron resonance (FTICR) data can generate an absorption-mode spectrum with much improved peak shape compared to the conventional magnitude-mode. However, research on phasing has been slow due to the complexity of the phase-wrapping problem. Recently, the method for phasing a broadband FTICR spectrum has been solved in the MS community which will surely resurrect this old topic. This paper provides a discussion on the data processing procedure of phase correction and features of the phase function based on both a mathematical treatment and experimental data. Finally, it is shown that the same phase function can be optimized by adding correction factors and can be applied from one experiment to another with different instrument parameters, regardless of the sample measured. Thus, in the vast majority of cases, the phase function needs to be calculated just once, whenever the instrument is calibrated.     

Impact of ion trap tandem mass spectra variability on the identification of peptides

Peptide identification based on tandem mass spectrometry and database searching algorithms has become one of the central technologies in proteomics. At the heart of this technology is the ability to reproducibly acquire high-quality tandem mass spectra for database interrogation. The variability in tandem mass spectra generation is often assumed to be minimal, and peptide identifications are typically based on a single tandem mass spectrum. In this paper, we characterize the variance of scores derived from replicate tandem mass spectra using several database search algorithms and demonstrate the effects of spectral variability on the correct identification of peptides. We show that the variance associated with the collection of tandem mass spectra can be substantial leading to sizable errors in search algorithm scores ( approximately 5-25% RSD) and ultimately incorrect assignments. Processing strategies are discussed to minimize the impact of tandem mass spectra variability on peptide identification.     

Ultratrace analysis based on Hadamard transform capillary electrophoresis

Hadamard transform capillary electrophoresis, which is based on a multiple sample injection technique, was combined with laser-induced fluorometry and utilized in the determination of analytes at subpicomolar levels. The sensitivity was substantially improved by increasing the order, i.e., the number of elements, of the Hadamard matrix. In fact, the signal-to-noise ratio was enhanced 18-fold by the use of a matrix of order 2047. A feasibility study was carried out by computer simulation to study the detection of an average of less than a single molecule in a single injection volume. The signal peak was clearly observable even under conditions at which only 0.3 molecule is present in the volume. Thus, this approach is potentially useful for ultratrace analysis, in which conventional single-injection capillary electrophoresis cannot be applied.