High-resolution Tandem Mass Spectra Research Articles

Critical evaluation of the use of artificial data for machine learning based de novo peptide identification

Proteins are essential components of all living cells and so the study of their in situ expression, proteomics, has wide reaching applications. Peptide identification in proteomics typically relies on matching high resolution tandem mass spectra to a protein database but can also be performed de novo. While artificial spectra have been successfully incorporated into database search pipelines to increase peptide identification rates, little work has been done to investigate the utility of artificial spectra in the context of de novo peptide identification. Here, we perform a critical analysis of the use of artificial data for the training and evaluation of de novo peptide identification algorithms. First, we classify the different fragment ion types present in real spectra and then estimate the number of spurious matches using random peptides. We then categorise the different types of noise present in real spectra. Finally, we transfer this knowledge to artificial data and test the performance of a state-of-the-art de novo peptide identification algorithm trained using artificial spectra with and without relevant noise addition. Noise supplementation increased artificial training data performance from 30% to 77% of real training data peptide recall. While real data performance was not fully replicated, this work provides the first steps towards an artificial spectrum framework for the training and evaluation of de novo peptide identification algorithms. Further enhanced artificial spectra may allow for more in depth analysis of de novo algorithms as well as alleviating the reliance on database searches for training data.

MS2Tox Machine Learning Tool for Predicting the Ecotoxicity of Unidentified Chemicals in Water by Nontarget LC-HRMS.

To achieve water quality objectives of the zero pollution action plan in Europe, rapid methods are needed to identify the presence of toxic substances in complex water samples. However, only a small fraction of chemicals detected with nontarget high-resolution mass spectrometry can be identified, and fewer have ecotoxicological data available. We hypothesized that ecotoxicological data could be predicted for unknown molecular features in data-rich high-resolution mass spectrometry (HRMS) spectra, thereby circumventing time-consuming steps of molecular identification and rapidly flagging molecules of potentially high toxicity in complex samples. Here, we present MS2Tox, a machine learning method, to predict the toxicity of unidentified chemicals based on high-resolution accurate mass tandem mass spectra (MS2). The MS2Tox model for fish toxicity was trained and tested on 647 lethal concentration (LC50) values from the CompTox database and validated for 219 chemicals and 420 MS2 spectra from MassBank. The root mean square error (RMSE) of MS2Tox predictions was below 0.89 log-mM, while the experimental repeatability of LC50 values in CompTox was 0.44 log-mM. MS2Tox allowed accurate prediction of fish LC50 values for 22 chemicals detected in water samples, and empirical evidence suggested the right directionality for another 68 chemicals. Moreover, by incorporating structural information, e.g., the presence of carbonyl-benzene, amide moieties, or hydroxyl groups, MS2Tox outperforms baseline models that use only the exact mass or log KOW.

In Vitro Metabolism Study of Seongsanamide A in Human Liver Microsomes Using Non-Targeted Metabolomics and Feature-Based Molecular Networking

Seongsanamide A is a bicyclic peptide with an isodityrosine residue discovered in Bacillus safensis KCTC 12796BP which exhibits anti-allergic activity in vitro and in vivo without significant cytotoxicity. The purpose of this study was to elucidate the in vitro metabolic pathway and potential for drug interactions of seongsanamide A in human liver microsomes using non-targeted metabolomics and feature-based molecular networking (FBMN) techniques. We identified four metabolites, and their structures were elucidated by interpretation of high-resolution tandem mass spectra. The primary metabolic pathway associated with seongsanamide A metabolism was hydroxylation and oxidative hydrolysis. A reaction phenotyping study was also performed using recombinant cytochrome P450 isoforms. CYP3A4 and CYP3A5 were identified as the major metabolic enzymes responsible for metabolite formation. Seongsanamide A did not inhibit the cytochrome P450 isoforms commonly involved in drug metabolism (IC50 > 10 µM). These results will contribute to further understanding the metabolism and drug interaction potential of various bicyclic peptides.

Non-target trend analysis for the identification of transformation products during ozonation experiments of citalopram and four of its biodegradation products

During ozonation in wastewater treatment plants, ozone reacts with emerging pollutants, which are partially removed through the secondary treatment, as long as, with their biotransformation products, triggering the formation of ozonation transformation products (TPs). Although the transformation of parent compounds (PCs) and their metabolites has been reported in the literature, the probable transformation of biotransformation products has not been investigated so far. This study evaluates the fate of citalopram (CTR) and four of its biotransformation products (DESCTR, CTRAM, CTRAC and CTROXO) during ozonation experiments. A Gaussian curve-based trend analysis was performed for the first time for the automated detection of TPs in ozone concentrations ranging from 0.06 to 12 mg/L. In total 46 ozonation TPs were detected; 7 TPs of CTR, 10 of DESCTR, 9 of CTRAM, 12 of CTRAC and 8 of CTROXO and were structurally elucidated based on their high resolution tandem mass spectra interpretation and tandem mass spectra similarity with the respective PC. Results have demonstrated that the examined compounds follow common transformation pathways in reaction with ozone and that common TPs were formed through the ozonation of different structurally-alike compounds. Moreover, the toxicity of the identified TPs was predicted with an in-house risk assessment program.

Differentiating Westlake Longjing tea from the first- and second-grade producing regions using ultra high performance liquid chromatography with quadrupole time-of-flight mass spectrometry-based untargeted metabolomics in combination with chemometrics.

There are numerous articles published for geographical discrimination of tea. However, few research works focused on the authentication and traceability of Westlake Longjing green tea from the first- and second-grade producing regions because the tea trees are planted in a limited growing zone with identical cultivate condition. In this work, a comprehensive analytical strategy was proposed by ultrahigh performance liquid chromatography-quadrupole time-of-flight mass spectrometry-based untargeted metabolomics coupled with chemometrics. The automatic untargeted data analysis strategy was introduced to screen metabolites that expressed significantly among different regions. Chromatographic features of metabolites can be automatically and efficiently extracted and registered. Meanwhile, those that were valuable for geographical origin discrimination were screened based on statistical analysis and contents in samples. Metabolite identification was performed based on high-resolution mass values and tandem mass spectra of screened peaks. Twenty metabolites were identified, based on which the two-way encoding partial least squares discrimination analysis was built for geographical origin prediction. Monte Caro simulation results indicated that prediction accuracy was up to 99%. Our strategy can be applicable for practical applications in the quality control of Westlake Longjing green tea.

In-Silico-Generated Library for Sensitive Detection of 2-Dimethylaminoethylamine Derivatized FAHFA Lipids Using High-Resolution Tandem Mass Spectrometry.

Fatty acid esters of hydroxy fatty acids (FAHFAs) are a family of recently discovered lipids with important physiological functions in mammals and plants. However, low detection sensitivity in negative ionization mode mass spectrometry makes low-abundance FAHFA challenging to analyze. A 2-dimethylaminoethylamine (DMED) based chemical derivatization strategy was recently reported to improve the MS sensitivity of FAHFAs by labeling FAHFAs with a positively ionizable tertiary amine group. To facilitate reliable, high-throughput, and automatic annotation of these compounds, a DMED-FAHFA in silico library containing 4290 high-resolution tandem mass spectra covering 264 different FAHFA classes was developed. The construction of the library was based on the heuristic information from MS/MS fragmentation patterns of DMED-FAHFA authentic standards, and then, the patterns were applied to computer-generated DMED-FAHFAs. The developed DMED-FAHFA in silico library was demonstrated to be compatible with library search software NIST MS Search and the LC-MS/MS data processing tool MS-DIAL to guarantee high-throughput and automatic annotations. Applying the in silico library in Arabidopsis thaliana samples for profiling FAHFAs by high-resolution LC-MS/MS enabled the annotation of 19 DMED-FAHFAs from 16 families, including 3 novel compounds. Using the in silico library largely decreased the false-positive annotation rate in comparison to low-resolution LC-MS/MS. The developed library, MS/MS spectra, and development templates are freely available for commercial and noncommercial use at https://zenodo.org/record/3606905.

Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes

The application of database search algorithms with very wide precursor mass tolerances for the “Open Search” paradigm has brought new efforts at post-translational modification discovery in shotgun proteomes. This approach has motivated the acceleration of database search tools by incorporating fragment indexing features. In this report, we compare open searches and sequence tag searches of high-resolution tandem mass spectra to seek a common “palette” of modifications when analyzing multiple formalin-fixed, paraffin-embedded (FFPE) tissues from Thermo Q-Exactive and SCIEX TripleTOF instruments. While open search in MSFragger produced some gains in identified spectra, careful FDR control limited the best result to 24% more spectra than narrow search (worst result: a loss of 9%). Open pFind produced high apparent sensitivity for PSMs, but entrapment sequences hinted that the actual error rate may be higher than reported by the software. Combining sequence tagging, open search, and chemical knowledge, we converged on this set of PTMs for our four FFPE sets: mono- and di-methylation (nTerm and Lys), single and double oxidation (Met and Pro), and variable carbamidomethylation (nTerm and Cys).

Molecular characterization of nonionic surfactant components of the Corexit® 9500 oil spill dispersant by high-resolution mass spectrometry.

Approximately 7 million liters of Corexit® dispersants were applied during the 2010 Deepwater Horizon oil spill to facilitate the dispersion of crude oil. At the time of application, the exact chemical composition of Corexit® was relatively unknown. Characterization of Corexit® 9500 was performed using high-resolution mass spectrometry to further understand the complexity of the nonionic surfactant components of this mixture. Corexit®9500 was analyzed by ultra-high-performance liquid chromatography (UHPLC) coupled to a high resolution Orbitrap Fusion Lumos mass spectrometer operated in positive electrospray ionization mode and a charged aerosol detector. Chromatographic conditions were optimized to efficiently separate isobaric and isomeric compounds. Polyethoxylated nonionic surfactants in Corexit® 9500 were identified using the following criteria: accurate mass (<3 ppm), retention time, and homologue series; in addition, interpretation of high-resolution tandem mass spectra was used to annotate tentative component structures. More than 2000 polysorbate nonionic surfactants in 87 homologue series were detected. Polysorbate surfactants were characterized by the type of molecular basis group (sorbitan, isosorbide, or fatty acid), degree of esterification (n= 0-4), ester chain length (C6-C24), and ester saturation, in addition to polydispersion by ethoxylation. Isomeric compounds were differentiated by LC/HRMS/MS analysis with product ion assignment. Results from the charged aerosol detector showed that the diesters (23.9 ± 0.78%) were the most abundant component in Corexit® 9500 followed by dioctyl sodium sulfosuccinate (DOSS) (19.2 ± 1.5%), triesters (17.3 ± 1.5%), and monoesters (15.7 ± 2.3%). Our analytical approach facilitated the characterization of polysorbate surfactants within Corexit® 9500 and allowed a systematic study to differentiate isomeric and isobaric compounds, when standards were not available. The characterized composition of Corexit® 9500 will facilitate future studies to determine the chemical and biological transformation kinetics and byproducts of Corexit® 9500 under environmental conditions.

Radical oxidation of methyl vinyl ketone and methacrolein in aqueous droplets: Characterization of organosulfates and atmospheric implications

In-cloud processing of volatile organic compounds is one of the significant routes leading to secondary organic aerosol (SOA) in the lower troposphere. In this study, we demonstrate that two atmospherically relevant α,β-unsaturated carbonyls, i.e., but-3-en-2-on (methyl vinyl ketone, MVK) and 2-methylopropenal (methacrolein, MACR), undergo sulfate radical-induced transformations in dilute aqueous systems under photochemical conditions to form organosulfates previously identified in ambient aerosols and SOA generated in smog chambers. The photooxidation was performed under sun irradiation in unbuffered aqueous solutions containing carbonyl precursors at a concentration of 0.2 mmol and peroxydisulfate as a source of sulfate radicals (SO4–) at a concentration of 0.95 mmol. UV–vis analysis of solutions showed the fast decay of unsaturated carbonyl precursors in the presence of sulfate radicals. The observation confirms the capacity of sulfate radicals to transform the organic compounds into SOA components in atmospheric waters. Detailed interpretation of high-resolution negative ion electrospray ionization tandem mass spectra allowed to assign molecular structures to multiple aqueous organosulfate products, including an abundant isoprene-derived organosulfate C4H8SO7 detected at m/z 199. The results highlight the solar aqueous-phase reactions as a potentially significant route for biogenic SOA production in clouds at locations where isoprene oxidation occurs. A recent modelling study suggests that such processes could likely contribute to 20–30 Tg year−1 production of SOA, referred to as aqSOA, which is a non-negligible addition to the still underestimated budget of atmospheric aerosol.

Forced and long-term degradation assays of tenoxicam, piroxicam and meloxicam in river water. Degradation products and adsorption to sediment

The fate of the pharmaceutical drugs tenoxicam, piroxicam and meloxicam in river water is evaluated here for first time. So, biological, photochemical and thermal degradation assays have been conducted to estimate their degradation rates and know their degradation products. Results indicated that the direct sunlight irradiation, without any protection, promoted a fast degradation of the oxicams while the chemical reactions in solution were less important. The biological degradation in water was negligible except for tenoxicam in whose case its influence was scarce. When the exposition of river water to sunlight was partially limited and kept under the natural day-night cycle, as occurs inside a body of water, tenoxicam, piroxicam and meloxicam (at 2 μg L−1) were detected during a period of 15, 27 and 45 days, respectively. Residues were monitored by ultra-pressure liquid chromatography/quadrupole time-of-flight/mass spectrometry after solid-phase extraction and several degradation products were found (10 for tenoxicam, 9 for piroxicam and 7 for meloxicam) and monitored over time. Their structures were proposed from the molecular formulae and fragmentation observed in high-resolution tandem mass spectra; the nature of the transformation products found in the long-term resulted to be very variable for each oxicam. Furthermore, the degradation in presence of river sediment was also monitored over time, with some differences being noted; the adsorption coefficients of the compounds on sediment were calculated, meloxicam exhibited a higher sorption capacity. The ecotoxicity of the different compounds in aquatic ecosystems was predicted, too.

Photochemical, thermal, biological and long-term degradation of celecoxib in river water. Degradation products and adsorption to sediment

Celecoxib is an anti-inflammatory drug with antibacterial activity whose fate in surface water is unknown. Thus, some assays have been conducted under forced biological, photochemical and thermal conditions, and non-forced conditions, to establish its persistence and degradation products in river water. The results suggest that celecoxib dissolved in river water is not biologically degraded while it is minimally altered after its exposure to sunlight or high temperature (70°C). Only the irradiation at 254nm promotes its complete degradation. Celecoxib is degraded about 3%, in 36 weeks, when water was kept at room temperature and the exposure to sunlight was partially limited as it happens inside a body of water. Residues were monitored by ultra-pressure liquid chromatography/quadrupole time-of-flight/mass spectrometry after solid-phase extraction; eleven degradation products were detected and the structures of nine of them were unequivocally proposed from the molecular formulae and fragmentation observed in high-resolution tandem mass spectra. The long-term transformation products under non-forced conditions were 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]benzenesulfonic acid, 4-[1-(4-sulfoaminephenyl)-3-(trifluoromethyl)-1H-pyrazol-5-yl]benzoic acid and a hydroxylated derivative. The degradation over time in presence of sediment was monitored, being slightly higher, about 4%. The adsorption equilibrium constants of celecoxib and degradation products on river sediment were estimated.

Collision-induced dissociation of phenethylamides: role of ion-neutral complexes.

Phenethylamides are a large group of naturally occurring molecules found both in the plant and animal kingdoms. In addition, they are used as intermediates for the synthesis of pharmaceutically important dihydro- and tetrahydroisoquinolines. To enable efficient characterization of this class of molecules, a detailed mass spectrometric fragmentation study of a broad series of analogs was carried out. The test compounds were synthesized using standard methods for amide bond formation. Low-energy high-resolution tandem mass spectra were acquired on a hybrid quadrupole/time-of-flight mass spectrometer using positive ion electrospray ionization. A total of 26 analogs were investigated in the study. Fragmentation of phenethylamides was found to proceed via intermediate ion-neutral complexes. The complexes can break down via multiple pathways including dissociation, proton transfer, Friedel-Crafts acylation, and single electron transfer. The relative contribution of each of these pathways strongly depends on the structure of the coupling amine and acid. A general scheme for the fragmentation of phenethylamides was developed. This study further extends the knowledge base of the ion-neutral complex by discovering Friedel-Crafts acylation as a novel reaction. The strong influence of minor structural modifications on the fragmentation patterns highlights the importance of testing many analogs in order to fully predict a fragmentation pattern of a particular class of molecules.

The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics.

We present a mass spectral library-based method to identify tandem mass spectra of peptides that contain unanticipated modifications and amino acid variants. We describe this as a "hybrid" method because it combines matching both ion m/z and mass losses. The mass loss is the difference between the mass of an ion peak and the mass of its precursor. This difference, termed DeltaMass, is used to shift the product ions in the library spectrum that contain the modification, thereby allowing library product ions that contain the unexpected modification to match the query spectrum. Clustered unidentified spectra from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and Chinese hamster ovary cells were used to evaluate this method. The results demonstrate the ability of the hybrid method to identify unanticipated modifications, insertions, and deletions, which may include those due to an incomplete protein sequence database or to search settings that exclude the correct identification, in high-resolution tandem mass spectra without regard to their precursor mass. This has been made possible by indexing of the m/z value of each fragment ion and its difference in mass from its precursor ion.

Persistence of alprazolam in river water according to forced and non-forced degradation assays: adsorption to sediment and long-term degradation products.

Alprazolam is a pharmaceutical compound that it is detected in surface waters. Some degradation studies in aqueous solutions and pharmaceutical products are available, but there is no reliable information about its stability in river water. Here, assays have been conducted under forced biological, photochemical, and thermal conditions, and under non-forced conditions, to estimate the fate of alprazolam in river water and know its degradation products. The forced assays indicated that the biological and photochemical degradation of alprazolam was negligible; heating at 70°C for a long time barely affected it. The degradation of alprazolam in river water at 100μg/L was about 5% after 36weeks, keeping the water under a natural day-night cycle at room temperature and limiting partially the exposure to sunlight as happens inside a body of water; no change in concentration was observed when the monitoring was performed at 2μg/L. The results suggest the persistence of alprazolam in surface water and a possible accumulation over time. Residues were monitored by ultra-pressure liquid chromatography/quadrupole time-of-flight/mass spectrometry after solid-phase extraction; nine degradation products were found and the structures for most of them were proposed from the molecular formulae and fragmentation observed in high-resolution tandem mass spectra. (5-chloro-2-(3-methyl-4H-1,2,4-triazol-4-yl)phenyl)(phenyl)methanol was the main long-term transformation product in conditions that simulate those in a mass of water. The degradation rate in presence of sediment was equally very low under non-forced conditions; adsorption coefficients of alprazolam and major degradation products were calculated. Copyright © 2016 John Wiley & Sons, Ltd.

GroupFilter: A software tool for efficient filtering of Morpheus search engine results

Morpheus is a search algorithm developed recently for high-resolution tandem mass spectra. According to the developers, its intrinsic property is discriminating short sequence length peptides. Therefore, elimination of direct comparisons between peptide spectrum matches (PSMs) for short and long peptides may potentially increase the search sensitivity for a given FDR level. In the proposed approach, all PSMs are grouped according to the number of matched fragment ions, followed by separate filtering of identifications in each group using target-decoy approach. The approach is applied to Morpheus output results and does not cause a significant increase in the overall data analysis time. The proposed approach was implemented as a Python command-line tool, called GroupFilter. Several data sets from different types of mass spectrometers were used for testing of the software, including the data from the original Morpheus search engine paper. Separate FDR filtering for grouped identifications increased the number of identified peptides by up to 18% compared with the default Morpheus post-processing procedure. The proposed approach can be considered as an addition to the Morpheus search engine.

Degradation of indomethacin in river water under stress and non-stress laboratory conditions: degradation products, long-term evolution and adsorption to sediment

The pharmaceutical compound indomethacin is not totally removed in wastewater treatment plants, whose effluents flow into aquatic environments; concentrations in the 0.1–100ng/L range are commonly found in surface waters, and its fate is unknown. Here, biological, photochemical and thermal degradation assays were conducted under stress and non-stress conditions to estimate its degradation rate in river water and establish its degradation products over time. The results revealed that direct sunlight irradiation promoted the complete degradation of indomethacin (2μg/L) in less than 6hr, but indomethacin was detected over a period of 4months when water was kept under the natural day–night cycle and the exposure to sunlight was partially limited, as occurs inside a body of water. The biological degradation in water was negligible, while the hydrolysis at pH7.8 was slow. Residues were monitored by ultra-pressure liquid chromatography/quadrupole time-of-flight/mass spectrometry after solid-phase extraction, and six degradation products were found; their structures were proposed based on the molecular formulae and fragmentation observed in high-resolution tandem mass spectra. 4-Chlorobenzoic and 2-acetamido-5-methoxybenzoic acids were the long-term transformation products, persisting for at least 30weeks in water kept under non-stress conditions. Furthermore, the degradation in the presence of sediment was also monitored over time, with some differences being noted. The adsorption coefficients of indomethacin and degradation products on river sediment were calculated; long-term degradation products did not have significant adsorption to sediment.

Fate of the drug chlorpromazine in river water according to laboratory assays. Identification and evolution over time of degradation products. Sorption to sediment

Toxic effects of the non-biodegradable drug chlorpromazine and its degradation products have been reported on microorganisms in aqueous media. Here, chlorpromazine degradation assays in forced and non-forced conditions have been done to know its persistence and degradation products in river water. Sunlight irradiation promotes the complete degradation of chlorpromazine (2 μg L−1) in less than 4 h, but if the exposure to sunlight is limited chlorpromazine is detected during 4 weeks in river water. Sixteen degradation products in surface water are described for first time after solid-phase extraction and analysis by ultra-pressure liquid chromatography/quadrupole time-of-flight/mass spectrometry; their structures are proposed from the molecular formulae of the fragment-ions observed in high-resolution tandem mass spectra. Hydroxylation and oxidation products such as chlorpromazine sulfoxide, 2-hydroxypromazine and 2-hydroxypromazine sulfoxide were predominant degradation products in the early stages; some benzo[1,4]thiazin-6-ol derivatives resulting from the breakdown of the phenothiazine core were the major and relatively stable products after 20 weeks under non-forced conditions. A degradation pathway of chlorpromazine in water is outlined. Moreover, it is shown that chlorpromazine is very strongly adsorbed on sediment while the degradation products that kept the promazine core have a notable capacity of sorption, too; sorption coefficients are calculated. Finally, a prediction about the toxicity of the degradation products in aquatic ecosystems suggests that some of them have toxicities similar, or even higher, than chlorpromazine.

Large-Scale Metabolite Analysis of Standards and Human Serum by Laser Desorption Ionization Mass Spectrometry from Silicon Nanopost Arrays.

The unique challenges presented by metabolomics have driven the development of new mass spectrometry (MS)-based techniques for small molecule analysis. We have previously demonstrated silicon nanopost arrays (NAPA) to be an effective substrate for laser desorption ionization (LDI) of small molecules for MS. However, the utility of NAPA-LDI-MS for a wide range of metabolite classes has not been investigated. Here we apply NAPA-LDI-MS to the large-scale acquisition of high-resolution mass spectra and tandem mass spectra from a collection of metabolite standards covering a range of compound classes including amino acids, nucleotides, carbohydrates, xenobiotics, lipids, and other classes. In untargeted analysis of metabolite standard mixtures, detection was achieved for 374 compounds and useful MS/MS spectra were obtained for 287 compounds, without individual optimization of ionization or fragmentation conditions. Metabolite detection was evaluated in the context of 31 metabolic pathways, and NAPA-LDI-MS was found to provide detection for 63% of investigated pathway metabolites. Individual, targeted analysis of the 20 common amino acids provided detection of 100% of the investigated compounds, demonstrating that improved coverage is possible through optimization and targeting of individual analytes or analyte classes. In direct analysis of aqueous and organic extracts from human serum samples, spectral features were assigned to a total of 108 small metabolites and lipids. Glucose and amino acids were quantitated within their physiological concentration ranges. The broad coverage demonstrated by this large-scale screening experiment opens the door for use of NAPA-LDI-MS in numerous metabolite analysis applications.

Neucode Labels for Multiplexed, Absolute Protein Quantification.

We describe a new method to accomplish multiplexed, absolute protein quantification in a targeted fashion. The approach draws upon the recently developed neutron encoding (NeuCode) metabolic labeling strategy and parallel reaction monitoring (PRM). Since PRM scanning relies upon high-resolution tandem mass spectra for targeted protein quantification, incorporation of multiple NeuCode labeled peptides permits high levels of multiplexing that can be accessed from high-resolution tandem mass spectra. Here we demonstrate this approach in cultured cells by monitoring a viral infection and the corresponding viral protein production over many infection time points in a single experiment. In this context the NeuCode PRM combination affords up to 30 channels of quantitative information in a single MS experiment.

MetFrag relaunched: incorporating strategies beyond in silico fragmentation.

BackgroundThe in silico fragmenter MetFrag, launched in 2010, was one of the first approaches combining compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data. Since then many new approaches have evolved, as has MetFrag itself. This article details the latest developments to MetFrag and its use in small molecule identification since the original publication.ResultsMetFrag has gone through algorithmic and scoring refinements. New features include the retrieval of reference, data source and patent information via ChemSpider and PubChem web services, as well as InChIKey filtering to reduce candidate redundancy due to stereoisomerism. Candidates can be filtered or scored differently based on criteria like occurence of certain elements and/or substructures prior to fragmentation, or presence in so-called “suspect lists”. Retention time information can now be calculated either within MetFrag with a sufficient amount of user-provided retention times, or incorporated separately as “user-defined scores” to be included in candidate ranking. The changes to MetFrag were evaluated on the original dataset as well as a dataset of 473 merged high resolution tandem mass spectra (HR-MS/MS) and compared with another open source in silico fragmenter, CFM-ID. Using HR-MS/MS information only, MetFrag2.2 and CFM-ID had 30 and 43 Top 1 ranks, respectively, using PubChem as a database. Including reference and retention information in MetFrag2.2 improved this to 420 and 336 Top 1 ranks with ChemSpider and PubChem (89 and 71 %), respectively, and even up to 343 Top 1 ranks (PubChem) when combining with CFM-ID. The optimal parameters and weights were verified using three additional datasets of 824 merged HR-MS/MS spectra in total. Further examples are given to demonstrate flexibility of the enhanced features.ConclusionsIn many cases additional information is available from the experimental context to add to small molecule identification, which is especially useful where the mass spectrum alone is not sufficient for candidate selection from a large number of candidates. The results achieved with MetFrag2.2 clearly show the benefit of considering this additional information. The new functions greatly enhance the chance of identification success and have been incorporated into a command line interface in a flexible way designed to be integrated into high throughput workflows. Feedback on the command line version of MetFrag2.2 available at http://c-ruttkies.github.io/MetFrag/ is welcome.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0115-9) contains supplementary material, which is available to authorized users.