A calibration method that simplifies and improves accurate determination of peptide molecular masses by MALDI-TOF MS

Improving mass accuracy in matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of pathogenic proteins using 6xHIS-tagged internal calibration

RATIONALE

Linear mode of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been routinely used for bacterial identification in the clinic, depending on the pattern analysis of spectral libraries rather than accurate mass measurement of ribosomal proteins (10-15 kDa). However, a demand for more accurate mass analysis of pathogens (e.g. KPC-2 carbapenemase) has been recently increasing for diagnostic purposes.

METHODS

We introduced a 6xHIS-tagged KPC-2 (i.e. hKPC-2) and used it as an internal mass calibrator for the mass calibration of target proteins. After internal mass calibration (In-Cal), we evaluated the observed mass of KPC-2 against the theoretical mass of hKPC-2, which has 823 Da mass difference from the target protein. We further assessed the accuracy and precision of our calibration method regarding the identification of KPC-2 and other pathogens in clinical isolates (n = 42).

RESULTS

Among several candidates for internal mass calibrators, the In-Cal using a 6xHIS-tagged protein on the target showed the highest mass accuracy and precision in the detection of target proteins (e.g. KPC-2). The application of hKPC-2 as an internal calibrator showed substantial improvement of mass accuracy, mass precision and also quantification of KPC in linearity and repeatability for KPC detection in the clinical isolates.

CONCLUSIONS

Our In-Cal method using 6xHIS-tagged protein in MALDI-TOFMS allows successful mass calibration (<3.5 Da) of pathogenic proteins (>20 kDa) and provides high mass accuracy as much as that of medium- and high-resolution mass spectrometry.

Comprehensive Lists of Internal Calibrants for Ultrahigh-Resolution Mass Spectrometry Analysis of Crude Oil and Natural Organic Matter and Their Preparation Recipes

In this work, comprehensive lists of internal calibrants for accurate mass determination of molecules in crude oils, natural organic matter, and soil as well as their preparation recipes are presented. The lists include various sets of chemicals for positive- and negative-ion mode electrospray ionization, atmospheric pressure chemical ionization, atmospheric pressure photoionization, and laser desorption ionization. The chemicals were chosen based on their solvent compatibility, ionization efficiency, and accessibility. The sample preparation process was optimized for each ionization method and type of sample. The lists include detailed information on preparation solvent, concentrations, and mixing ratios of sample and calibrants. Internal calibration using the information in the lists results in successful calibration, and all the data presented in this study show root-mean-square errors between the theoretical and obtained m/z numbers of less than 0.4 ppm. The information presented in this study provides an important guideline for researchers working on complex mixtures with ultrahigh-resolution mass spectrometry.

A Method for Defining the Position of Ion Formation in a MALDI TOFMS by Analysis of the Laser Image on the Sample Surface

A method is developed to determine the position of ion formation along the flight axis of a MALDI TOFMS instrument using the image of the laser on the sample surface. Previous work (JASMS 2018, 29, 422-434) showed that misalignment of the sample stage in a Bruker Autoflex III MALDI TOFMS as well as multiple insertions/mountings of the target plate and differences in target plate shape itself produced reproducible changes in the measured ion time-of-flight which could be attributed to changes in the position of ion formation along the instrument flight axis. Here, a small but reproducible change in the position of the laser in the sample-viewing camera image was observed, with the movement depending on both the sample position and target plate used. Using the change in coordinates of the laser position in the camera image and the known angle of incidence of the laser on the sample surface, the initial z-axis position of the ion at different locations on the plate can be calculated, exactly defining changes in the ion flight path length and the distance between the sample plate and first extraction plate/grid with sample position on the target plate. A correction method is developed to correct the time-of-flight values collected from different locations on the sample plate using the laser images, with the relative standard deviation (RSD) being reduced from 23 ppm to below 6 ppm. The laser images, along with the measured target plate heights, are also used to calculate the misalignment of the sample stage. Graphical Abstract.

Diagnosing and Correcting Mass Accuracy and Signal Intensity Error Due to Initial Ion Position Variations in a MALDI TOFMS

Frustrated by worse than expected error for both peak area and time-of-flight (TOF) in matrix assisted laser desorption ionization (MALDI) experiments using samples prepared by electrospray deposition, it was finally determined that there was a correlation between sample location on the target plate and the measured TOF/peak area. Variations in both TOF and peak area were found to be due to small differences in the initial position of ions formed in the source region of the TOF mass spectrometer. These differences arise largely from misalignment of the instrument sample stage, with a smaller contribution arising from the non-ideal shape of the target plates used. By physically measuring the target plates used and comparing TOF data collected from three different instruments, an estimate of the magnitude and direction of the sample stage misalignment was determined for each of the instruments. A correction method was developed to correct the TOFs and peak areas obtained for a given combination of target plate and instrument. Two correction factors are determined, one by initially collecting spectra from each sample position used and another by using spectra from a single position for each set of samples on a target plate. For TOF and mass values, use of the correction factor reduced the error by a factor of 4, with the relative standard deviation (RSD) of the corrected masses being reduced to 12-24 ppm. For the peak areas, the RSD was reduced from 28% to 16% for samples deposited twice onto two target plates over two days. Graphical Abstract.

Supplementation of enzyme-treated soy protein saves dietary protein and promotes digestive and absorptive ability referring to TOR signaling in juvenile fish

This study was conducted to evaluate the effect of enzyme-treated soy protein (ETSP) supplementation in the low-protein diet on growth performance, digestive and absorptive capacities, and related signaling molecules' gene expressions in juvenile Jian carp. The results showed that percent weight gain (PWG), specific growth rate (SGR), and feed intake (FI) were decreased by reducing dietary protein from 34 to 32% (P < 0.05). Supplying low-protein diet with optimal ETSP increased previously mentioned indices of juvenile Jian carp (P < 0.05), which also had no significant difference with the high-protein diet (34%CP) (P > 0.05). Compared with the low-protein diet, appropriate ETSP supplementation in the low-protein diet increased (P < 0.05) (1) the trypsin, lipase, and amylase activities in the hepatopancreas; (2) cholecystokinin concentration in the proximal intestine; (3) the γ-glutamyl transpeptidase (γ-GT), alkaline phosphatase (AKP), and Na⁺/K⁺-ATPase activities in all intestinal segments; and (4) the messenger RNA (mRNA) levels of trypsin, lipase, and amylase in hepatopancreas and γ-GT in the mid (MI) and distal (DI) intestine, alkaline phosphatase in MI, and Na⁺/K⁺-ATPase and target of rapamycin in all intestinal segments. At the same time, appropriate ETSP supplementation in the low-protein diet downregulated the mRNA levels of AKP in the DI and eIF4E-binding protein 2 in all intestinal segments (P < 0.05). In conclusion, adding 10 g ETSP/kg diet in the low-protein diet can restore the growth performance and digestive and absorptive abilities to the levels in group with 34% dietary protein. Supplementation of optimal ETSP in the low-protein diet enhanced the digestive and absorptive abilities and regulated the signaling molecules related to the TOR signaling pathway.

Applications of Mass Spectrometry Imaging to Cancer

Pathologists play an essential role in the diagnosis and prognosis of benign and cancerous tumors. Clinicians provide tissue samples, for example, from a biopsy, which are then processed and thin sections are placed onto glass slides, followed by staining of the tissue with visible dyes. Upon processing and microscopic examination, a pathology report is provided, which relies on the pathologist's interpretation of the phenotypical presentation of the tissue. Targeted analysis of single proteins provide further insight and together with clinical data these results influence clinical decision making. Recent developments in mass spectrometry facilitate the collection of molecular information about such tissue specimens. These relatively new techniques generate label-free mass spectra across tissue sections providing nonbiased, nontargeted molecular information. At each pixel with spatial coordinates (x/y) a mass spectrum is acquired. The acquired mass spectrums can be visualized as intensity maps displaying the distribution of single m/z values of interest. Based on the sample preparation, proteins, peptides, lipids, small molecules, or glycans can be analyzed. The generated intensity maps/images allow new insights into tumor tissues. The technique has the ability to detect and characterize tumor cells and their environment in a spatial context and combined with histological staining, can be used to aid pathologists and clinicians in the diagnosis and management of cancer. Moreover, such data may help classify patients to aid therapy decisions and predict outcomes. The novel complementary mass spectrometry-based methods described in this chapter will contribute to the transformation of pathology services around the world.

Improved mass resolution and mass accuracy in TOF-SIMS spectra and images using argon gas cluster ion beams

The popularity of argon gas cluster ion beams (Ar-GCIB) as primary ion beams in time-of-flight secondary ion mass spectrometry (TOF-SIMS) has increased because the molecular ions of large organic- and biomolecules can be detected with less damage to the sample surfaces. However, Ar-GCIB is limited by poor mass resolution as well as poor mass accuracy. The inferior quality of the mass resolution in a TOF-SIMS spectrum obtained by using Ar-GCIB compared to the one obtained by a bismuth liquid metal cluster ion beam and others makes it difficult to identify unknown peaks because of the mass interference from the neighboring peaks. However, in this study, the authors demonstrate improved mass resolution in TOF-SIMS using Ar-GCIB through the delayed extraction of secondary ions, a method typically used in TOF mass spectrometry to increase mass resolution. As for poor mass accuracy, although mass calibration using internal peaks with low mass such as hydrogen and carbon is a common approach in TOF-SIMS, it is unsuited to the present study because of the disappearance of the low-mass peaks in the delayed extraction mode. To resolve this issue, external mass calibration, another regularly used method in TOF-MS, was adapted to enhance mass accuracy in the spectrum and image generated by TOF-SIMS using Ar-GCIB in the delayed extraction mode. By producing spectra analyses of a peptide mixture and bovine serum albumin protein digested with trypsin, along with image analyses of rat brain samples, the authors demonstrate for the first time the enhancement of mass resolution and mass accuracy for the purpose of analyzing large biomolecules in TOF-SIMS using Ar-GCIB through the use of delayed extraction and external mass calibration.

Commercial formaldehyde standard for mass calibration in mass spectrometry

Common calibration standards for mass spectrometry can be a source of many problems including instrument contamination, ionization suppression and formation of unidentified ions during subsequent analysis. In this article, we present a new approach for the calibration of mass analyzers such as a quadrupole-time-of-flight mass spectrometry using a diluted solution of commercial formaldehyde. Formaldehyde is an inexpensive and commonly used solvent, and its intrinsic polymerization leads to the formation of polyoxymethylene (POM) oligomers, which are excellent multiple calibration standards for a low-mass spectral region (up to m/z 400) in the positive and negative mode of electrospray ionization. We explore the nature and origin of these polymeric species and attributed them to chemical reactions of formaldehyde and stabilizing agents in commercial formaldehyde solutions and during electrospray ionization. In contrast to other calibrants, POM oligomers do not contaminate the instrument and can easily be removed from the sample delivery system. Using tandem mass spectrometry, we elucidate the structures of the detected POM oligomers and report their reference masses, which are tightly spaced by 30 mass units. In our calibration method, mass errors of <5 ppm can be obtained from m/z 20-400 using external calibration with a simple one-point zero-order correction of spectral data and without the need for operation of a dual spray or internal calibrants. Our approach will be particularly useful for those interested in the analysis of fragile ions with low m/z values and can function at instrumental conditions required for analysis of the most labile metabolites and environmental contaminants.

Mass accuracy improvement of reversed-phase liquid chromatography/electrospray ionization mass spectrometry based urinary metabolomic analysis by post-run calibration using sodium formate cluster ions

RATIONALE

Typically, a batch metabolomics analysis using liquid chromatography/electrospray ionization time-of-flight mass spectrometry (LC/ESI-TOF MS) takes 2 to 3 days. However, the mass accuracy - which has an important influence on metabolite identification - can drift by as much as about 17 ppm in such a time period. In an untargeted urinary metabolomics analysis by reversed-phase liquid chromatography (RPLC)/ESI-MS, the signals of sodium formate cluster ions were detected at the column-washing step. The cluster ions were used to calibrate the mass spectrometer for more accurate detection.

METHODS

The spectra were calibrated post-run by the sodium formate cluster ions, which were used as the internal standard, in order to improve the mass accuracy.

RESULTS

In the analysis of urine samples, we calibrated the spectra acquired by the micrOTOF with the sodium cluster ions. In positive mode ESI, the average errors of these cluster ions were improved to ±0.48 ppm and in negative mode ESI, to ±0.94 ppm after calibration. The mass accuracy remained within ±0.01 ppm over the duration of 6.25 days. An error window of 4 ppm appears to be suitable for metabolite identification when using post-calibration.

CONCLUSIONS

The results showed that sodium formate cluster ions could be utilized for the calibration of LC/ESI-TOF MS and the average instrumental errors could be maintained at low levels for long-term analyses. This method could be applied not only to urine sample, but also to low sodium samples, such as saliva, by dissolving the sample in 1 μM sodium formate solution. This method provides a good solution for accurate mass detection of metabolomic analysis.

PAS-cal: A repetitive peptide sequence calibration standard for MALDI mass spectrometry

Mass spectrometers equipped with matrix-assisted laser desorption/ionization (MALDI-MS) require frequent multipoint calibration to obtain good mass accuracy over a wide mass range and across large numbers of samples. In this study, we introduce a new synthetic peptide mass calibration standard termed PAS-cal tailored for MALDI-MS based bottom-up proteomics. This standard consists of 30 peptides between 8 and 37 amino acids long and each constructed to contain repetitive sequences of Pro, Ala and Ser as well as one C-terminal arginine residue. MALDI spectra thus cover a mass range between 750 and 3200 m/z in MS mode and between 100 and 3200 m/z in MS/MS mode. Our results show that multipoint calibration of MS spectra using PAS-cal peptides compares well to current commercial reagents for protein identification by PMF. Calibration of tandem mass spectra from LC-MALDI experiments using the longest peptide, PAS-cal37, resulted in smaller fragment ion mass errors, more matching fragment ions and more protein and peptide identifications compared to commercial standards, making the PAS-cal standard generically useful for bottom-up proteomics.

A new, modular mass calibrant for high-mass MALDI-MS

The application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the analysis of high-mass proteins requires suitable calibration standards at high m/z ratios. Several possible candidates were investigated, and concatenated polyproteins based on recombinantly expressed maltodextrin-binding protein (MBP) are shown here to be well-suited for this purpose. Introduction of two specific recognition sites into the primary sequence of the polyprotein allows for the selective cleavage of MBP3 into MBP and MBP2. Moreover, these MBP2 and MBP3 oligomers can be dimerized specifically, such that generation of MPB4 and MBP6 is possible as well. With the set of calibrants presented here, the m/z range of 40-400 kDa is covered. Since all calibrants consist of the same species and differ only in mass, the ionization efficiency is expected to be similar. However, equimolar mixtures of these proteins did not yield equal signal intensities on a detector specifically designed for detecting high-mass molecules.

Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis

Biological systems are increasingly being studied in a holistic manner, using omics approaches, to provide quantitative and qualitative descriptions of the diverse collection of cellular components. Among the omics approaches, metabolomics, which deals with the quantitative global profiling of small molecules or metabolites, is being used extensively to explore the dynamic response of living systems, such as organelles, cells, tissues, organs and whole organisms, under diverse physiological and pathological conditions. This technology is now used routinely in a number of applications, including basic and clinical research, agriculture, microbiology, food science, nutrition, pharmaceutical research, environmental science and the development of biofuels. Of the multiple analytical platforms available to perform such analyses, nuclear magnetic resonance and mass spectrometry have come to dominate, owing to the high resolution and large datasets that can be generated with these techniques. The large multidimensional datasets that result from such studies must be processed and analyzed to render this data meaningful. Thus, bioinformatics tools are essential for the efficient processing of huge datasets, the characterization of the detected signals, and to align multiple datasets and their features. This paper provides a state-of-the-art overview of the data processing tools available, and reviews a collection of recent reports on the topic. Data conversion, pre-processing, alignment, normalization and statistical analysis are introduced, with their advantages and disadvantages, and comparisons are made to guide the reader.

Generation of CsI cluster ions for mass calibration in matrix-assisted laser desorption/ionization mass spectrometry

A simple method was developed for the generation of cesium iodide (CsI) cluster ions up to m/z over 20,000 in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Calibration ions in both positive and negative ion modes can readily be generated from a single MALDI spot of CsI(3) with 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene] malononitrile (DCTB) matrix. The major cluster ion series observed in the positive ion mode is [(CsI)(n)Cs](+), and in the negative ion mode is [(CsI)(n)I](-). In both cluster series, ions spread evenly every 259.81 units. The easy method described here for the production of CsI cluster ions should be useful for MALDI MS calibrations.

Elemental sulfur as a versatile low-mass-range calibration standard for laser desorption ionization mass spectrometry

Facile generation of series of singly charged radical anions (S(n)(-*); n = 1-15) and cations (S(n)(+*); n = 2-11) by direct laser ionization renders elemental sulfur an excellent material for the low-mass-region calibration of time of flight (TOF) mass spectrometers. Upon irradiation by a 337-nm UV laser, elemental sulfur undergoes facile ionization without the need of an additional laser-absorbing matrix. An intense and evenly spaced set of peaks is obtained in both modes.

Binding of S-methyl-5'-thioadenosine and S-adenosyl-L-methionine to protein MJ0100 triggers an open-to-closed conformational change in its CBS motif pair

Cystathionine beta-synthase (CBS) domains are small motifs that are present in proteins with completely different functions. Several genetic diseases in humans have been associated with mutations in their sequence, which has made them promising targets for rational drug design. The protein MJ0100 from Methanocaldococcus jannaschii includes a DUF39 domain of so far unknown function and a CBS domain pair (Bateman domain) at its C-terminus. This work presents the crystallographic analysis of four different states of the CBS motif pair of MJ0100 in complex with different numbers of S-adenosyl-L-methionine (SAM) and S-methyl-5'-thioadenosine (MTA) ligands, providing evidence that ligand-induced conformational reorganization of Bateman domain dimers could be an important regulatory mechanism. These observations are in contrast to what is known from most of the other Bateman domain structures but are supported by recent studies on the magnesium transporter MgtE. Our structures represent the first example of a CBS domain protein complexed with SAM and/or MTA and might provide a structural basis for understanding the molecular mechanisms regulated by SAM upon binding to the C-terminal domain of human CBS, whose structure remains unknown.

Laser desorption ionization of red phosphorus clusters and their use for mass calibration in time-of-flight mass spectrometry

Phosphorus clusters P(n) (n = 1-89) are easily formed from red phosphorus by laser desorption ionization (LDI) and they cover a range of up to approx. m/z 3000 in both positive and negative ion mode. The clusters are singly charged and the spectra are simple because phosphorus is monoisotopic. The mass spectra can be measured with an acceptable resolution and intensity. The use of positively charged P(n) clusters for calibration in mass spectrometry was examined and it was demonstrated that in external calibration a standard deviation of +/-0.04 m/z units can be achieved even when using a common commercial matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrument. When used as internal standards the P(n) clusters react with some analytes - C(60) and C(70) fullerenes and cucurbituril[8], for example. It was also found that red phosphorus is a suitable MALDI matrix for peptides and proteins, illustrated by the examples of a Calmix mixture of bradykinin, angiotensin, renin, adrenocorticotropic hormone ACTH fragment 18-359 and insulin, and of insulin alone.

Profiling and imaging of lipids on brain and liver tissue by matrix-assisted laser desorption/ ionization mass spectrometry using 2-mercaptobenzothiazole as a matrix

2-Mercaptobenzothiazole (MBT) is employed for the first time as a matrix for the analysis of lipids from tissue extracts using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We demonstrate that the performance of MBT is superior to that of the matrixes commonly employed for lipids, due to its low vapor pressure, its low acidity, and the formation of small crystals, although because of the strong background at low m/z, it precludes detection of species below approximately 500 Da. This inconvenience can be partly overcome with the formation of Cs adducts. Using a polymer-based dual calibration, a mass accuracy of approximately 10 ppm in lipid extracts and of approximately 80 ppm in tissues is achieved. We present spectra from liver and brain lipid extracts where a large amount of lipid species is identified, in both positive and negative ion modes, with high reproducibility. In addition, the above-mentioned special properties of MBT allow its employment for imaging mass spectrometry. In the present work, images of brain and liver tissues showing different lipid species are presented, demonstrating the advantages of the employment of MBT.

SALAMI (Spectrum ALignments using high Accuracy Mass and hIgh sensitivity data): how to make the best out of hybrid MS/MS data

We present a software algorithm that combines ion trap and orbitrap product ion spectra acquired in parallel. The hybrid product ion spectra identify more peptides than when using two separate searches for the orbitrap and LTQ data. The program extracts the high-accuracy mass data from the Orbitrap mass analyzer and combines it with the high-sensitivity data analyzed in the LTQ linear ion trap; the m/z values of the high-confidence fragment ions are corrected to orbitrap mass accuracies and the fragment ion intensities are amplified. This approach utilizes the parallel spectrum measurement capabilities of the LTQ-Orbitrap. We present our approach to handling this type of hybrid data, explain our alignment program, and discuss the advantages of the chosen methodology.

Combinatorial approaches for mass spectra recalibration

Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger datasets, the automated recalibration of mass spectra becomes important to ensure that every peak in the sample spectrum is correctly assigned to some peptide and protein. Algorithms for recalibrating mass spectra have to be robust with respect to wrongly assigned peaks, as well as efficient due to the amount of mass spectrometry data. The recalibration of mass spectra leads us to the problem of finding an optimal matching between mass spectra under measurement errors. We have developed two deterministic methods that allow robust computation of such a matching: The first approach uses a computational geometry interpretation of the problem, and tries to find two parallel lines with constant distance that stab a maximal number of points in the plane. The second approach is based on finding a maximal common approximate subsequence, and improves existing algorithms by one order of magnitude exploiting the sequential nature of the matching problem. We compare our results to a computational geometry algorithm using a topological line-sweep.

Allergy to human seminal fluid: cross-reactivity with dog dander

BACKGROUND

Human seminal plasma (HSP) allergy is uncommon, with symptoms ranging from vulvovaginal pruritus to life-threatening anaphylaxis. Although several seminal plasma allergens have been reported and their molecular masses have been estimated to range between 12 and 75 kd, the prostate-specific antigen (PSA) has recently been identified as a causative allergen. Given that in a large number of cases symptoms appeared during or after the first intercourse, a cross-reactivity phenomenon might be implicated.

OBJECTIVE

We sought to assess the presence of IgE cross-reactivity among proteins from dog epithelium and HSP and to attempt to identify the allergens involved.

METHODS

Forty-one patients with dog epithelium allergy were selected. One of them experienced anaphylaxis in contact with her husband's seminal plasma. Skin prick tests, serum specific IgE measurements, SDS-PAGE immunoblotting, and inhibition tests were performed to study the pattern of IgE-binding proteins and the potential cross-reactivity between HSP and dog epithelium. Mass spectrometry was carried out to identify the protein involved in allergy reactions.

RESULTS

Twenty-four percent of the sera from patients with dog epithelium allergy recognized an IgE-binding band of 28 kd in HSP immunoblotting. Mass spectrometry identified this band as the PSA. SDS-PAGE immunoblotting-inhibition showed a complete IgE-binding inhibition when sera from these patients were preincubated with dog dander extract.

CONCLUSIONS

IgE cross-reactivity among proteins from dog dander and human PSA is demonstrated.

High-throughput axial MALDI-TOF MS using a 2-kHz repetition rate laser

A high-throughput axial MALDI-TOF mass spectrometer utilizing a laser with a 2-kHz pulse repetition-rate was constructed and tested. This fast mass spectrometer provided a data acquisition rate 10 times faster than a commercially available (200 Hz) axial mass spectrometer, while maintaining comparable limits of detection (200 amol of Glu fib peptide). Mass resolution, only slightly less than the commercial instrument (10 000 vs 14 000), was sufficient for baseline resolution of isotopic clusters of peptides with m/z <2700. A new method of mass calibration, which combined a limited number of internal and external standards, provided the same 15 ppm mass accuracy over the entire sample plate on either instrument. Implementing the 2-kHz laser required a faster data acquisition system and high-voltage pulse electronics, together with a novel strategy for rapid sample plate movements during acquisition, to achieve a sample analysis rate of up to 2 spots/s (with 800 shots/spot). The overall performance of the fast MALDI-TOF MS instrument was demonstrated by the acquisition, in 12 min, of an LC-MS data set from a plate of 625 fractions collected during LC separation of an 16O/18O differentially labeled proteomic sample of a tryptic digest of an E. coli lysate.

Renal cathepsin G and angiotensin II generation

BACKGROUND

Alternative pathways of angiotensin II biosynthesis play a significant role in the renin-angiotensin system. In this study porcine renal tissue was investigated for angiotensin II-generating enzymes.

METHODS AND RESULTS

Protein extracts from porcine renal tissue were fractionated by liquid chromatography and tested for their angiotensin II-generating activity by the mass-spectrometry-assisted enzyme screening system (MES) and the active fractions were purified to near homogeneity. In one of these active fractions, inhibitable by an angiotensin-converting enzyme specific inhibitor, purified by anion-exchange chromatography, followed by hydroxyapatite chromatography, lectin affinity chromatography, size-exclusion chromatography and two-dimensional electrophoresis, angiotensin-converting enzyme was identified by a tryptic peptide matrix-assisted-laser-desorption/ionization (MALDI) mass fingerprint analysis. In a second active fraction, which was inhibited by chymostatin and antipain, yielded by anion-exchange chromatography, followed by hydroxyapatite chromatography, lectin affinity chromatography, chymostatin-antipain chromatography and one-dimensional electrophoresis, cathepsin G was identified by electro-spray ionization (ESI)-ion-trap mass spectrometry. The angiotensin-generating activities of the fraction containing angiotensin-converting enzyme and the fraction containing cathepsin G were in the same order of magnitude, thus showing that the contribution of cathepsin G towards the production of angiotensin II is significant.

CONCLUSION

This is the first time that cathepsin G has been identified in mammalian renal tissue.

A New Analytical Material-Enhanced Laser Desorption Ionization (MELDI) Based Approach for the Determination of Low-Mass Serum Constituents Using Fullerene Derivatives for Selective Enrichment

60]fullerene derivatives (dioctadecyl methano[60]fullerene, [60]fullerenoacetic acid, and IDA-[60]fullerene) were prepared and subjected to a comprehensive characterization study including protein binding properties and capacity. These fullerene derivatives were successfully applied as material-enhanced laser desorption/ionization (MELDI) carrier materials. It is shown that diverse functionalities result in characteristic human serum peak patterns (m/z 2000-20 000) in terms of signal intensity as well as the number of detectable masses. In addition, the fullerene derivatives clearly provided differences in the low molecular weight mass region (m/z 1000-4000) after elution of the adsorbed serum constituents, and [60]fullerenoacetic acid was the most effective carrier material. Novel high-speed, monolithic, high-resolution capillary columns, prepared by thermally initiated copolymerization of methylstyrene (MSt) and 1,2-bis(p-vinylphenyl)ethane (BVPE) were employed for eluate separation and target spotting. Thus, serum compounds in the low-mass range were successfully fractionated and subjected to MALDI-MS/MS analysis. This contribution, hence, proposes a new "top-down" strategy for proteome research enabling protein profiling as well as biomarker identification in the low-mass range using selective enrichment, high-resolution separation, and offline MALDI-MS/MS evaluation.

Analytical model of peptide mass cluster centres with applications

Background

The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate peptide mass lists, to identify and remove non-peptide peaks and for data reduction.

Results

We developed an analytical model of the peptide mass cluster centres. Inputs to the model included, the amino acid frequencies in the sequence database, the average length of the proteins in the database, the cleavage specificity of the proteolytic enzyme used and the cleavage probability. We examined the accuracy of our model by comparing it with the model based on an in silico sequence database digest. To identify the crucial parameters we analysed how the cluster centre location depends on the inputs. The distance to the nearest cluster was used to calibrate mass spectrometric peptide peak-lists and to identify non-peptide peaks.

Conclusion

The model introduced here enables us to predict the location of the peptide mass cluster centres. It explains how the location of the cluster centres depends on the input parameters. Fast and efficient calibration and filtering of non-peptide peaks is achieved by a distance measure suggested by Wool and Smilansky.

De novo analysis of peptide tandem mass spectra by spectral graph partitioning

We report on a new de novo peptide sequencing algorithm that uses spectral graph partitioning. In this approach, relationships between m/z peaks are represented by attractive and repulsive springs, and the vibrational modes of the spring system are used to infer information about the peaks (such as "likely b-ion" or "likely y-ion"). We demonstrate the effectiveness of this approach by comparison with other de novo sequencers on test sets of ion-trap and QTOF spectra, including spectra of mixtures of peptides. On all datasets, we outperform the other sequencers. Along with spectral graph theory techniques, the new de novo sequencer EigenMS incorporates another improvement of independent interest: robust statistical methods for recalibration of time-of-flight mass measurements. Robust recalibration greatly outperforms simple least-squares recalibration, achieving about three times the accuracy for one QTOF dataset.

Processing and classification of protein mass spectra

Among the many applications of mass spectrometry, biomarker pattern discovery from protein mass spectra has aroused considerable interest in the past few years. While research efforts have raised hopes of early and less invasive diagnosis, they have also brought to light the many issues to be tackled before mass-spectra-based proteomic patterns become routine clinical tools. Known issues cover the entire pipeline leading from sample collection through mass spectrometry analytics to biomarker pattern extraction, validation, and interpretation. This study focuses on the data-analytical phase, which takes as input mass spectra of biological specimens and discovers patterns of peak masses and intensities that discriminate between different pathological states. We survey current work and investigate computational issues concerning the different stages of the knowledge discovery process: exploratory analysis, quality control, and diverse transforms of mass spectra, followed by further dimensionality reduction, classification, and model evaluation. We conclude after a brief discussion of the critical biomedical task of analyzing discovered discriminatory patterns to identify their component proteins as well as interpret and validate their biological implications.

Standardization of calibration and quality control using surface enhanced laser desorption ionization-time of flight-mass spectrometry

BACKGROUND

Protein profiling by surface enhanced laser desorption ionization-time of flight-mass spectrometry (SELDI-TOF-MS) is gaining importance as a diagnostic tool for a whole range of diseases. This report describes a QC procedure, which acts prospectively by checking the calibration before starting profiling experiments.

METHODS

A well-defined protocol for calibration of the Protein Biosystem IIc instrument was established, using a commercial QC sample containing independent certified standards and by determination of acceptance criteria. Instrument calibration was performed externally every week with the standards provided by the manufacturer. QC was performed for the period of 5 months.

RESULTS

According to the acceptance criteria defined in this study, data points should be in the established range of the process mean+/-2 standard deviations for the mass-to-charge ratios (m/z values), peak intensities, signal-to-noise ratios (S/N), and peak resolutions for insulin and apomyoglobin in the QC sample. Moreover, it was demonstrated that the pipetting variability in the handling of the QC sample significantly contributed to systematic errors and that spotting of a larger volume of QC sample resulted in a better reproducibility.

CONCLUSIONS

Stringent quality control of the calibration part of SELDI-TOF-MS experiments prevents unreliable data acquisition from the very start.

Optimizing search conditions for the mass fingerprint-based identification of proteins

The two central problems in protein identification by searching a protein sequence collection with MS data are the optimal use of experimental information to allow for identification of low abundance proteins and the accurate assignment of the probability that a result is false. For comprehensive MS-based protein identification, it is necessary to choose an appropriate algorithm and optimal search conditions. We report a systematic study of the quality of PMF-based protein identifications under different sequence collection search conditions using the Probability algorithm, which assigns the statistical significance to each result. We employed 2244 PMFs from 2-DE-separated human blood plasma proteins, and performed identification under various search constraints: mass accuracy (0.01-0.3 Da), maximum number of missed cleavage sites (0-2), and size of the sequence collection searched (5.6 x 10(4)-1.8 x 10(5)). By counting the number of significant results (significance levels 0.05, 0.01, and 0.001) for each condition, we demonstrate the search condition impact on the successful outcome of proteome analysis experiments. A mass correction procedure utilizing mass deviations of albumin matching peptides was tested in an attempt to improve the statistical significance of identifications and iterative searching was employed for identification of multiple proteins from each PMF.

Universal metrics for quality assessment of protein identifications by mass spectrometry

Increasing numbers of large proteomic datasets are becoming available. As attempts are made to interpret these datasets and integrate them with other forms of genomic data, researchers are becoming more aware of the importance of data quality with respect to protein identification. We present three simple and universal metrics that describe different aspects of the quality of protein identifications by peptide mass fingerprinting. Hit ratio gives an indication of the signal-to-noise ratio in a mass spectrum, mass coverage measures the amount of protein sequence matched, and excess of limit-digested peptides reflects the completeness of the digestion that precedes the peptide mass fingerprinting. Receiver-operating characteristic plots show that the novel metric, excess of limit-digested peptides, can discriminate between correct and random matches more accurately than search score when validating the results from a state-of-the-art protein identification software system (Mascot) especially when combined with the two other metrics, hit ratio and mass coverage. Recommendations are made regarding the use of the metrics when reporting protein identification experiments.

Method for qualitative comparisons of protein mixtures based on enzyme-catalyzed stable-isotope incorporation

Determining which proteins are unique among one or several protein populations is an often-encountered task in proteomics. To this purpose, we present a new method based on trypsin-catalyzed incorporation of the stabile isotope (18)O in the C-termini of tryptic peptides, followed by LC-MALDI MS analysis. The analytical strategy was designed such that proteins unique to a given population out of several can be assigned in a single experiment by the isotopic signal intensity distributions of their tryptic peptides in the recorded mass spectra. The method is demonstrated for protein-protein interaction analysis, in which the differential isotope labeling was used to distinguish endogenous human brain proteins interacting with a recombinant bait protein from nonbiospecific background binders.

A proteomic method for the analysis of changes in protein concentrations in response to systemic perturbations using metabolic incorporation of stable isotopes and mass spectrometry

While several techniques exist for assessing quantitative differences among proteomes representing different cell states, methods for assessing how these differences are mediated are largely missing. We present a method that allows one to differentiate between cellular processes, such as protein synthesis, degradation and PTMs which affect protein concentrations. An induced systemic perturbation of a cell culture was coupled to a replacement of the growth medium to one highly enriched in the stable isotope 15N. The relative abundance of the 15N- and 14N-enriched forms of proteins, isolated from cell cultures harvested at time points following the onset of the perturbation, were determined by MS. Alterations in protein synthesis and degradation were quantified by comparing proteins isolated from perturbed and unperturbed cultures, respectively. The method was evaluated by subjecting HeLa cells to heat stress. As expected, a number of known heat shock proteins (Hsp) increased in concentration during heat stress. For Hsp27, increased de novo synthesis accounted for the concentration increase, while for Hsp70, decreased degradation accounted for the increase. A protein that was detected only after prolonged heat stress, vimentin, was not primarily synthesized de novo, but appeared rather as a result of PTM.

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process

Background:

Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is called a peak-list. In order to classify the underlying amino acid sequence, the acquired spectra are usually compared with synthetic ones. Development of suitable methods of direct peak-list comparison may be advantageous for many applications.

Results:

The pairwise peak-list comparison is a multistage process composed of matching of peaks embedded in two peak-lists, normalisation, scaling of peak intensities and dissimilarity measures. In our analysis, we focused on binary and intensity based measures. We have modified the measures in order to comprise the mass spectrometry specific properties of mass measurement accuracy and non-matching peaks. We compared the labelling of peak-list pairs, obtained using different factors of the pairwise peak-list comparison, as being the same or different to those determined by sequence database searches. In order to elucidate how these factors influence the peak-list comparison we adopted an analysis of variance type method with the partial area under the ROC curve as a dependent variable.

Conclusion:

The analysis of variance provides insight into the relevance of various factors influencing the outcome of the pairwise peak-list comparison. For large MS/MS and PMF data sets the outcome of ANOVA analysis was consistent, providing a strong indication that the results presented here might be valid for many various types of peptide mass measurements.

Analysis of NOD2-mediated proteome response to muramyl dipeptide in HEK293 cells

NOD2, a cytosolic receptor for the bacterial proteoglycan fragment muramyl dipeptide (MDP), plays an important role in the recognition of intracellular pathogens. Variants in the bacterial sensor domain of NOD2 are genetically associated with an increased risk for the development of Crohn disease, a human chronic inflammatory bowel disease. In the present study, global protein expression changes after MDP stimulation were analyzed by two-dimensional PAGE of total protein extracts of human cultured cells stably transfected with expression constructs encoding for wild type NOD2 (NOD2(WT)) or the disease-associated NOD2 L1007fsinsC (NOD2(SNP13)) variant. Differentially regulated proteins were identified by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) peptide mass fingerprinting and MALDI MS/MS. The limited overlap in the responses of the NOD2-overexpressing cell lines to MDP included a down-regulation of heat shock 70-kDa protein 4. A complex pro-inflammatory program regulated by NOD2(WT) that encompasses a regulation of key genes involved in protein folding, DNA repair, cellular redox homeostasis, and metabolism was observed both under normal growth conditions and after stimulation with MDP. By using the comparison of NOD2(WT) and disease-associated NOD2(SNP13) variant, we have identified a proteomic signature pattern that may further our understanding of the influence of genetic variations in the NOD2 gene in the pathophysiology of chronic inflammatory bowel disease.

Experiments in searching small proteins in unannotated large eukaryotic genomes

There is growing interest to use mass spectrometry data to search genome sequences directly. Previous work by other authors demonstrated that this approach is able to correct and complement available genome annotations. We discuss the practical difficulty of searching large eukaryotic genomes with peptide ion trap tandem mass spectra of small proteins (<40 kDa). The challenging problem of automatically identifying peptides that span across exon/intron boundaries is explored for the first time by using experimental data. In a human genome search, we find that roughly 30% of the peptides are missed, due to various reasons, compared to a Swiss-Prot search. We show that this percentage is significantly reduced with improved parent mass accuracy. We finally provide several examples of predicted gene structures that could be improved by proteomics data, in particular by peptides spanning across exon/intron boundaries.

Structural characterization of chelator-terminated dendrimers and their synthetic intermediates by mass spectrometry

Herein, we report the structural analysis of a novel family of iron-chelating dendrimers and their synthetic intermediates utilizing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and electrospray ionization ion trap (ESI IT) MS. These dendrimers share a benzene tricarbonyl core moiety attached to three tripodal branching units, each linking to three terminal groups, ranging from carboxyl, catechol and 3-hydroxy-6-methyl-pyran-4-one moieties and their protected analogs. In order to monitor the progression of dendrimer synthesis, all intermediates and final products were mass analyzed by conventional MALDI-TOF MS with and without alkali metal spiking. For structural characterization, interpretable post-source decay (PSD) and electrospray ionization ion trap MS/MS spectra were obtained from proton, sodium and potassium adducts of the dendrimers. One major route of dendrimer fragmentation was at or adjacent to the amide bonds either of the terminal chelating groups or near the core moiety. Fragmentation in the latter case was primarily at the N-terminal side of the amide bond and was directed by the proximity of a tertiary carbon of the branching unit. Furthermore, it was found that terminal ester, ether and amide linkages to the protecting and chelating groups could be sequentially broken in a single MS/MS spectrum through multiple cleavages resulting in product ions of decreasing intensity. Moreover, such cleavages could also be induced in a stepwise manner in a multistage ion trap MS(n) experiment.

Towards the proteome of the marine bacteriumRhodopirellula baltica: Mapping the soluble proteins

The marine bacterium Rhodopirellula baltica, a member of the phylum Planctomycetes, has distinct morphological properties and contributes to remineralization of biomass in the natural environment. On the basis of its recently determined complete genome we investigated its proteome by 2-DE and established a reference 2-DE gel for the soluble protein fraction. Approximately 1000 protein spots were excised from a colloidal Coomassie-stained gel (pH 4-7), analyzed by MALDI-MS and identified by PMF. The non-redundant data set contained 626 distinct protein spots, corresponding to 558 different genes. The identified proteins were classified into role categories according to their predicted functions. The experimentally determined and the theoretically predicted proteomes were compared. Proteins, which were most abundant in 2-DE gels and the coding genes of which were also predicted to be highly expressed, could be linked mainly to housekeeping functions in glycolysis, tricarboxic acid cycle, amino acid biosynthesis, protein quality control and translation. Absence of predictable signal peptides indicated a localization of these proteins in the intracellular compartment, the pirellulosome. Among the identified proteins, 146 contained a predicted signal peptide suggesting their translocation. Some proteins were detected in more than one spot on the gel, indicating post-translational modification. In addition to identifying proteins present in the published sequence database for R. baltica, an alternative approach was used, in which the mass spectrometric data was searched against a maximal ORF set, allowing the identification of four previously unpredicted ORFs. The 2-DE reference map presented here will serve as framework for further experiments to study differential gene expression of R. baltica in response to external stimuli or cellular development and compartmentalization.

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants

BACKGROUND

Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses.

RESULTS

We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from http://www.bioconductor.org.

CONCLUSION

The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5-15%.

Chip with twin anchors for reduced ion suppression and improved mass accuracy in MALDI-TOF mass spectrometry

A new sample target for matrix-assisted laser desorption/ionization mass spectrometry is described. The target consists of pairs of elevated hydrophilic anchor surfaces, positioned in proximity onto a microchip. The anchors are used to obtain separate preparations of sample and external standard, while both anchor surfaces are irradiated simultaneously by the laser pulse. Using a standard, based on six peptides, a 2-fold improvement in mass accuracy is observed. Also, ion suppression is significantly reduced. With a one peptide calibration standard, 22 tryptic fragments from a BSA digest are detected using the twin-anchor concept, whereas only 14 fragments are detected when the sample and standard are laser-ablated as a mixture from a conventional anchor target. A volume of approximately 30 pL of sample solution of angiotensin I is transferred to the anchor surface, under a thin layer of a perfluorocarbon, to prevent a concentration bias due to evaporation. With this arrangement, a detection limit of 1.5 amol was achieved with a signal-to-noise ratio of 22:1.

Proteome analysis ofArabidopsis thaliana by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry

In the present study we show results of a large-scale proteome analysis of the recently sequenced plant Arabidopsis thaliana. On the basis of a previously published sequential protein extraction protocol, we prepared protein extracts from eight different A. thaliana tissues (primary leaf, leaf, stem, silique, seedling, seed, root, and inflorescence) and analysed these by two-dimensional gel electrophoresis. A total of 6000 protein spots, from three of these tissues, namely primary leaf, silique and seedling, were excised and the contained proteins were analysed by matrix assisted laser desorption/ionisation time of flight mass spectrometry peptide mass fingerprinting. This resulted in the identification of the proteins contained in 2943 spots, which were found to be products of 663 different genes. In this report we present and discuss the methodological and biological results of our plant proteome analysis.

High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome

Proteomic studies have addressed the composition of plant chloroplast ribosomes and 70S ribosomes from the unicellular organism Chlamydomonas reinhardtii But comprehensive characterization of cytoplasmic 80S ribosomes from higher plants has been lacking. We have used two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) to analyse the cytoplasmic 80S ribosomes from the model flowering plant Arabidopsis thaliana. Of the 80 ribosomal protein families predicted to comprise the cytoplasmic 80S ribosome, we have confirmed the presence of 61; specifically, 27 (84%) of the small 40S subunit and 34 (71%) of the large 60S subunit. Nearly half (45%) of the ribosomal proteins identified are represented by two or more distinct spots in the 2-DE gel indicating that these proteins are either post-translationally modified or present as different isoforms. Consistently, MS-based protein identification revealed that at least one-third (34%) of the identified ribosomal protein families showed expression of two or more family members. In addition, we have identified a number of non-ribosomal proteins that co-migrate with the plant 80S ribosomes during gradient centrifugation suggesting their possible association with the 80S ribosomes. Among them, RACK1 has recently been proposed to be a ribosome-associated protein that promotes efficient translation in yeast. The study, thus provides the basis for further investigation into the function of the other identified non-ribosomal proteins as well as the biological meaning of the various ribosomal protein isoforms.

Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein-DNA interactions

To gain insights into complex biological processes, such as transcription and replication, the analysis of protein-DNA interactions and the determination of their sequence requirements are of central importance. In this study, we probed protein microarray technology and ultraviolet crosslinking combined with mass spectrometry (MS) for their practicability to study protein-DNA interactions. We chose as a model system the well-characterized interaction of bacterial replication initiator DnaA with its cognate binding site, the DnaA box. Interactions of DnaA domain 4 with a high-affinity DnaA box (R4) and with a low-affinity DnaA box (R3) were compared. A mutant DnaA domain 4, A440V, was included in the study. DnaA domain 4, wt, spotted onto FAST slides, revealed a strong signal only with a Cy5-labeled, double-stranded, 21-mer oligonucleotide containing DnaA box R4. No signals were obtained when applying the mutant protein. Ultraviolet crosslinking combined with nanoLC/MALDI-TOF MS located the site of interaction to a peptide spanning amino acids 433- 442 of Escherichia coli DnaA. This fragment contains six residues that were identified as being involved in DNA binding by recently published crystal structure and nuclear magnetic resonance (NMR) analysis. In the future, the technologies applied in this study will become important tools for studying protein-DNA interactions.