Confirmation of the full conversion of ethylene oxide to 2-chloroethanol in fumigated foodstuffs: possible implications for risk assessment.

This study describes the extension of a gas chromatography mass spectrometry (GC-MS) method, initially devoted to the analysis of ethylene oxide (EO) in ice cream, to a larger range of food items including herbs, spices, vegetables, inorganic salts, food supplements, thickeners, etc. Results are reported as EOTotal according to EC 2015/868 definition (expressed as EO equivalents as the sum of native EO and 2-chloroethanol (2-CE) after acidic hydrolysis) with a limit of quantification at 0.01 mg/kg regardless of the food item. Its ruggedness was demonstrated through fortification experiments on hundreds of samples. Re-analysis of 146 positive food samples without hydrolysis demonstrated that not EO but 2-CE is the predominant analyte detected in the different processed ingredients suspected to have been previously treated with EO. A series of eight contaminated dried herbs and spices were also re-analysed by four ISO 17025 accredited commercial laboratories making use of different analytical strategies for EO determination in foods. Each laboratory reported EOTotal levels within the same concentration range, but the resulting reproducibility ranged from 23% to 41% depending on the sample. Additionally, we show that results of free EO from methods based on conversion to 2-iodoethanol may lead to artefactual detection of native EO (false positive). An official method of analysis applicable for different food matrices would be useful to avoid discrepancies of results. Altogether, these data re-enforce the fact that in absence of native EO in food items, risk assessment of EO in foodstuffs should consider the predominance of 2-CE. A toxicological risk assessment using the food additive xanthan gum as a case study is discussed.

Detection and characterization of small-sized microplastics (≥ 5 µm) in milk products.

Microplastics (MPs) have gained a high degree of public interest since they are associated with the global release of plastics into the environment. Various studies have confirmed the presence of MPs throughout the food chain. However, information on the ingestion of MPs via the consumption of many commonly consumed foods like dairy products are scarce due to the lack of studies investigating the "contamination" of this food group by MPs. This lack of occurrence data is mainly due to the absence of robust analytical methods capable of reliably quantifying MPs with size < 20 µm in foods. In this work, a new methodology was developed to accurately determine and characterize MPs in milk-based products using micro-Raman (µRaman) technology, entailing combined enzymatic and chemical digestion steps. This is the first time that the presence of relatively low amounts of small-sized MP (≥ 5 µm) have been reported in raw milk collected at farm just after the milking machine and in some processed commercial liquid and powdered cow's milk products.

Peptide Characterization and Functional Stability of a Partially Hydrolyzed Whey-Based Formula over Time.

Human clinical trials have shown that a specific partially hydrolyzed 100% whey-based infant formula (pHF-W) reduces AD risk in the first yeast of life. Meta-analyses with a specific pHF-W (pHF-W1) confirm a protective effect while other meta-analyses pooling different pHF-W show conflicting results. Here we investigated the molecular composition and functional properties of the specific pHF-W1 as well as the stability of its manufacturing process over time. This specific pHF-W1 was compared with other pHF-Ws. We used size exclusion chromatography to characterize the peptide molecular weight (MW), a rat basophil degranulation assay to assess the relative level of beta-lactoglobulin (BLG) allergenicity and a preclinical model of oral tolerance induction to test prevention of allergic sensitization. To analyze the exact peptide sequences before and after an HLA binding assay, a mass cytometry approach was used. Peptide size allergenicity and oral tolerance induction were conserved across pHF-W1 batches of production and time. The median MW of the 37 samples of pHF-W1 tested was 800 ± 400 Da. Further oral tolerance induction was observed using 10 different batches of the pHF-W1 with a mean reduction of BLG-specific IgE levels of 0.76 log (95% CI = -0.95; -0.57). When comparing pHF-W1 with three other formulas (pHF-W2 3 and 4), peptide size was not necessarily associated with allergenicity reduction in vitro nor oral tolerance induction in vivo as measured by specific IgE level (p < 0.05 for pHF-W1 and 2 and p = 0.271 and p = 0.189 for pHF-W3 and 4 respectively). Peptide composition showed a limited overlap between the formulas tested ranging from 11.7% to 24.2%. Furthermore nine regions in the BLG sequence were identified as binding HLA-DR. In conclusion, not all pHF-Ws tested have the same peptide size distribution decreased allergenicity and ability to induce oral tolerance. Specific peptides are released during the different processes used by different infant formula producers.

Analysis of ethylene oxide in ice creams manufactured with contaminated carob bean gum (E410).

Residues of ethylene oxide (EO), a banned fumigant in the EU, were found at amounts above the maximum residue limit (MRL) in carob (locust) bean gum (additive E410). The pesticide entered the food chain via stabiliser blends that are used as minor ingredients in the manufacture of ice cream. Consequently, all products that contained the non-compliant ingredient were withdrawn or recalled in several countries across the EU, in most cases irrespective of whether the pesticide residue was detectable or not in the final product. This is the first report of a reliable method to determine EO and its metabolite/marker compound 2-chloroethanol (2-CE), either together or independently in ice cream, with a limit of quantification at 0.01 mg EO/kg and recovery in the range of 87-104% across the levels investigated (0.01, 0.02 and 0.06 mg EO/kg). The method applies QuEChERS extraction and isotope dilution gas chromatography coupled with tandem mass spectrometry (GC-MS/MS). High resolution mass spectrometry (HRMS) confirmed the specificity of low mass ions. Data on the stability of EO and 2-CE under thermal conditions revealed that 2-CE is relatively stable in an ice cream matrix (ca. 80% recovery of spiked material). Importantly, this study also demonstrates that not EO, but 2-CE is the predominant analyte detected in the contaminated samples, which is new information of significance in terms of the overall risk assessment of EO in foodstuffs.

High resolution mass spectrometry workflow for the analysis of food contaminants: Application to plant toxins, mycotoxins and phytoestrogens in plant-based ingredients.

An analytical workflow including mass spectral library, generic sample preparation, chromatographic separation, and analysis by high-resolution mass spectrometry (HRMS) was developed to gain insight into the occurrence of plant toxins, mycotoxins and phytoestrogens in plant-based food. This workflow was applied to 156 compounds including 90 plant toxins (pyrrolizidine alkaloids, tropane alkaloids, glycoalkaloids, isoquinoline alkaloids and aristolochic acids), 54 mycotoxins (including ergot alkaloids and Alternaria toxins) and 12 phytoestrogens (including isoflavones, lignans and coumestan) in plant-based protein ingredients, cereal and pseudo-cereal products. A mass spectral library was built based on fragmentation spectra collected at 10 different collision energies in both positive and negative ionisation modes for each toxin. Emphasis was put on a generic QuEChERS-like sample preparation followed by ultra-high-pressure liquid chromatography using alkaline mobile phase allowing the separation of more than 50 toxic pyrrolizidine alkaloids. HRMS acquisition comprised a full-scan event for toxins detection followed by data-dependent MS2 for toxin identification against mass spectrum. Method performance was evaluated using fortified samples in terms of sensitivity, repeatability, reproducibility and recovery. All toxins were positively identified at levels ranging from 1 µg kg-1 to 100 µg kg-1. Quantitative results obtained by a standard addition approach met SANTE/12682/2019 criteria for 132 out of 156 toxins. Such a workflow using generic, sensitive and selective multi-residue method allows a better insight into the occurrence of regulated and non-regulated toxins in plant-based foods and to conduct safety evaluation and risk assessments when needed.

Handheld Spectral Sensing Devices Should Not Mislead Consumers as Far as Non-Authentic Food Is Concerned: A Case Study with Adulteration of Milk Powder.

With the rising trend of consumers being offered by start-up companies portable devices and applications for checking quality of purchased products, it appears of paramount importance to assess the reliability of miniaturized sensors embedded in such devices. Here, eight sensors were assessed for food fraud applications in skimmed milk powder. The performance was evaluated with dry- and wet-blended powders mimicking adulterated materials by addition of either ammonium sulfate, semicarbazide, or cornstarch in the range 0.5-10% of profit. The quality of the spectra was assessed for an adequate identification of the outliers prior to a deep assessment of performance for both non-targeted (soft independent modelling of class analogy, SIMCA) and targeted analyses (partial least square regression with orthogonal signal correction, OPLS). Here, we show that the sensors have generally difficulties in detecting adulterants at ca. 5% supplementation, and often fail in achieving adequate specificity and detection capability. This is a concern as they may mislead future users, particularly consumers, if they are intended to be developed for handheld devices available publicly in smartphone-based applications.

Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry.

Here we used a data-independent acquisition (DIA) method, Precursor Acquisition Independent from Ion Count (PAcIFIC), to systematically profile the S. cerevisiae proteome. Direct PAcIFIC analysis of a yeast whole cell lysate (WCL) yielded 90% reproducibility between replicates and detected approximately 2000 proteins. When combined with sub-cellular fractionation, reproducibility was equally high and the number of detected yeast proteins approached 5000. As noted previously, this unbiased DIA approach identified so-called "orphan" peptides that could only be detected by tandem mass spectra because there was no detectable precursor ion. Using this unique dataset we examined features associated with peptide detectability and demonstrated that orphans were more likely to arise from low copy number proteins than proteins with median or high copy number. Finally, an investigation into why some orphans also arose from high copy number proteins found that, aside from protein copy number, there was a bias toward physiochemical factors associated with regions flanking the proteolytic cleavage sites of orphan peptides. This suggested that those orphan peptides originating from high abundance proteins were likely the result of inefficient protease release, which has implications for quantitative bottom-up proteomics.

Low-allergenic hydrolyzed egg induces oral tolerance in mice.

BACKGROUND: Egg allergy is one of the most common food allergies in children. The standard therapy for egg allergy is strict avoidance. Yet, there is considerable clinical and scientific interest in primary or secondary prevention. A major drawback of oral tolerance (OT) induction protocols, however, is the possibility of severe side effects; thus, we have formulated a hypoallergenic egg product and demonstrate its in vivo capacity to modulate the immune system in the current study. METHODS: Hydrolyzed egg (HE) was produced using a combination of moderate heat treatment and enzymatic hydrolysis. The capacity of HE to induce OT was tested in experimental models and compared to whole egg (WE). Delayed-type hypersensitivity (DTH) responses, immune markers and potential early markers of OT were analyzed. RESULTS: Allergic responses, assessed by both DTH responses upon OVA challenge and serum OVA-specific IgE and IgG1, were decreased after treatment with HE and WE compared to the control group. Additionally, feeding WE and HE significantly decreased Th2 cytokine induction and cell proliferation, induced the activation of effector CD4+ T cells and increased numbers and percentages of ICOS+CD4+CD25+Foxp3+ cells. Furthermore, DO11.10 mouse experiments showed that HE contains other peptides than the OVA323-339 peptide that are able to induce tolerance to OVA. CONCLUSIONS: Altogether, results showed that HE induces OT in mice in a dose-dependent manner. Due to its low allergenicity compared to WE, it may represent a safer alternative for OT induction in at-risk subjects or oral immunotherapy in allergic patients.

Food peptidomics: large scale analysis of small bioactive peptides--a pilot study.

Food peptidomics deals in part with the identification and quantification of nutritionally relevant peptides which are called bioactive peptides. This category of peptides comprises large, medium to small peptides. However, small peptides (2-6 amino acids) represent by far the largest category. Such molecules sit at the interface of both the world of proteomics and small molecule. The purpose of this study was to evaluate the feasibility of developing an LC-MSMS based method to measure such small peptides at a large scale that is representative of the hundreds of known small bioactive peptides. In order to do that we selected a very complex and homogeneous peptide set in terms of chemical and physical properties. This peptide set comprised only di, tri- and tetrapeptides made out of the three branched chain amino acids (valine, leucine and isoleucine). Results showed that at least 60% of these 117 peptides can be uniquely identified although many are isobaric and co-eluting. Moreover, identical results were obtained when spiked into a complex matrix, i.e. hydrolyzed whey protein. In conclusion, these results support the feasibility of a large scale approach and open the door to further development for all potential small bioactive peptides known so far. BIOLOGICAL SIGNIFICANCE: Bioactive peptides are a key category of molecules for functional food application. Most known bioactive peptides are small (less than 5 amino acids) and hence represent a challenge in terms of analysis when using current proteomics techniques. Therefore development of the food peptidomics field through high throughput large scale assays for these molecules is mandatory in the future to better conduct research in this field.

Urinary proteome analysis of irritable bowel syndrome (IBS) symptom subgroups.

Irritable bowel syndrome (IBS) is a functional gastrointestinal (GI) disorder characterized by chronic abdominal pain associated with alterations in bowel function. Given the heterogeneity of the symptoms, multiple pathophysiologic factors are suspected to play a role. We classified women with IBS into four subgroups based on distinct symptom profiles. In-depth shotgun proteomic analysis was carried out to profile the urinary proteomes to identify possible proteins associated with these subgroups. First void urine samples with urine creatinine level≥100 mg/dL were used after excluding samples that tested positive for blood. Urine from 10 subjects representing each symptom subgroup was pooled for proteomic analysis. The urine proteome was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using a data-independent method known as Precursor Acquisition Independent From Ion Count (PAcIFIC) that allowed extended detectable dynamic range. Differences in protein quantities were determined by peptide spectral counting followed by validation of select proteins with ELISA or a targeted single reaction monitoring (LC-SRM/MS) approach. Four IBS symptom subgroups were selected: (1) Constipation, (2) Diarrhea+Low Pain, (3) Diarrhea+High Pain, and (4) High Pain+High Psychological Distress. A fifth group consisted of Healthy Control subjects. From comparisons of quantitative spectral counting data among the symptom subgroups and controls, a total of 18 proteins that showed quantitative differences in relative abundance and possible physiological relevance to IBS were selected for further investigation. Three of the 18 proteins were chosen for validation by either ELISA or SRM. An elevated expression of gelsolin (GSN) was associated with the high pain groups. Trefoil Factor 3 (TFF3) levels were higher in IBS groups compared to controls. In this study, the IBS patients subclassified by predominant symptoms showed differences in urine proteome levels. Proteins showing distinctive changes are involved in homeostasis of intestinal function and inflammatory response. These findings warrant future studies with larger, independent cohorts to enable more extensive assessment and validation of urinary protein markers as a diagnostic tool in adults with IBS.

Proteomic and transcriptomic profiling of Staphylococcus aureus surface LPXTG-proteins: correlation with agr genotypes and adherence phenotypes.

Staphylococcus aureus infections involve numerous adhesins and toxins, which expression depends on complex regulatory networks. Adhesins include a family of surface proteins covalently attached to the peptidoglycan via a conserved LPXTG motif. Here we determined the protein and mRNA expression of LPXTG-proteins of S. aureus Newman in time-course experiments, and their relation to fibrinogen adherence in vitro. Experiments were performed with mutants in the global accessory-gene regulator (agr), surface protein A (Spa), and fibrinogen-binding protein A (ClfA), as well as during growth in iron-rich or iron-poor media. Surface proteins were recovered by trypsin-shaving of live bacteria. Released peptides were analyzed by liquid chromatography coupled to tandem mass-spectrometry. To unambiguously identify peptides unique to LPXTG-proteins, the analytical conditions were refined using a reference library of S. aureus LPXTG-proteins heterogeneously expressed in surrogate Lactococcus lactis. Transcriptomes were determined by microarrays. Sixteen of the 18 LPXTG-proteins present in S. aureus Newman were detected by proteomics. Nine LPXTG-proteins showed a bell-shape agr-like expression that was abrogated in agr-negative mutants including Spa, fibronectin-binding protein A (FnBPA), ClfA, iron-binding IsdA, and IsdB, immunomodulator SasH, functionally uncharacterized SasD, biofilm-related SasG and methicillin resistance-related FmtB. However, only Spa and SasH modified their proteomic and mRNA profiles in parallel in the parent and its agr- mutant, whereas all other LPXTG-proteins modified their proteomic profiles independently of their mRNA. Moreover, ClfA became highly transcribed and active in fibrinogen-adherence tests during late growth (24 h), whereas it remained poorly detected by proteomics. On the other hand, iron-regulated IsdA-B-C increased their protein expression by >10-times in iron-poor conditions. Thus, proteomic, transcriptomic, and adherence-phenotype demonstrated differential profiles in S. aureus. Moreover, trypsin peptide signatures suggested differential protein domain exposures in various environments, which might be relevant for anti-adhesin vaccines. A comprehensive understanding of the S. aureus physiology should integrate all three approaches.

Mass spectrometry for nutritional peptidomics: How to analyze food bioactives and their health effects.

We describe nutritional peptidomics for discovery and validation of bioactive food peptide and their health effects. Understanding nature and bioactivity of nutritional peptides means comprehending an important level of environmental regulation of the human genome, because diet is the environmental factor with the most profound life-long influence on health. We approach the theme from three angles, namely the analysis, the discovery and the biology perspective. Food peptides derive from parent food proteins via in vitro hydrolysis (processing) or in vivo digestion by various unspecific and specific proteases, as opposed to the tryptic peptides typically generated in biomarker proteomics. A food bioactive peptide may be rare or unique in terms of sequence and modification, and many food genomes are less well annotated than e.g. the human genome. Bioactive peptides can be discovered either empirically or by prediction: we explain both the classical hydrolysis strategy and the bioinformatics-driven reversed genome engineering. In order to exert bioactivity, food peptides must be either ingested and then reach the intestine in their intact form or be liberated in situ from their parent proteins to act locally, that is in the gut, or even systemically, i.e. through the blood stream. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.

Quantitative mass spectrometry analysis using PAcIFIC for the identification of plasma diagnostic biomarkers for abdominal aortic aneurysm.

BACKGROUND: Abdominal aortic aneurysm (AAA) is characterized by increased aortic vessel wall diameter (>1.5 times normal) and loss of parallelism. This disease is responsible for 1-4% mortality occurring on rupture in males older than 65 years. Due to its asymptomatic nature, proteomic techniques were used to search for diagnostic biomarkers that might allow surgical intervention under nonlife threatening conditions. METHODOLOGY/PRINCIPAL FINDINGS: Pooled human plasma samples of 17 AAA and 17 control patients were depleted of the most abundant proteins and compared using a data-independent shotgun proteomic strategy, Precursor Acquisition Independent From Ion Count (PAcIFIC), combined with spectral counting and isobaric tandem mass tags. Both quantitative methods collectively identified 80 proteins as statistically differentially abundant between AAA and control patients. Among differentially abundant proteins, a subgroup of 19 was selected according to Gene Ontology classification and implication in AAA for verification by Western blot (WB) in the same 34 individual plasma samples that comprised the pools. From the 19 proteins, 12 were detected by WB. Five of them were verified to be differentially up-regulated in individual plasma of AAA patients: adiponectin, extracellular superoxide dismutase, protein AMBP, kallistatin and carboxypeptidase B2. CONCLUSIONS/SIGNIFICANCE: Plasma depletion of high abundance proteins combined with quantitative PAcIFIC analysis offered an efficient and sensitive tool for the screening of new potential biomarkers of AAA. However, WB analysis to verify the 19 PAcIFIC identified proteins of interest proved inconclusive save for five proteins. We discuss these five in terms of their potential relevance as biological markers for use in AAA screening of population at risk.

Data-independent proteomic screen identifies novel tamoxifen agonist that mediates drug resistance.

A label-free quantitative variation of the recently developed data-independent shotgun proteomic method precursor acquisition independent from ion count (PAcIFIC) was used to identify novel proteins implicated in cancer progression and resistance. Specifically, this screen identified the pro-metastatic protein anterior gradient 2 (AGR2) as significantly up-regulated in tamoxifen-treated cells. Highlighting the need for direct proteome profiling methods like PAcIFIC, neither data-dependent gas-phase fractionation nor a transcriptomic screen detected AGR2 protein/transcript at significantly up-regulated levels. Further cell-based experiments using human cancer cell lines and in vivo xenografts confirmed the PAcIFIC hypothesis that AGR2 is up-regulated in MCF-7 cells post tamoxifen treatment and that it is implicated in drug resistance mediation.

Faster, quantitative, and accurate precursor acquisition independent from ion count.

Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, this bottom-up method presents major drawbacks in terms of detectable dynamic range. Recently, we demonstrated the superior performance of a data-independent method we termed precursor acquisition independent from ion count (PAcIFIC). Here, we report a faster, accurate, multiplexed, and quantitative PAcIFIC method. Our results show that the time needed to perform such analysis can be decreased by 33% to 66% using modern ion trap instruments and that high mass accuracy can be applied to such a strategy. Quantification capability is demonstrated on protein standards and a whole bacterial cell lysate using isobaric tagging. Finally, we confirm in yeast the dynamic range capabilities of such a method where proteins down to less than 50 copies per cell can be monitored without sample prefractionation.

Time-resolved quantitative proteome analysis of in vivo intestinal development.

Postnatal intestinal development is a very dynamic process characterized by substantial morphological changes that coincide with functional adaption to the nutritional change from a diet rich in fat (milk) to a diet rich in carbohydrates on from weaning. Time-resolved studies of intestinal development have so far been limited to investigation at the transcription level or to single or few proteins at a time. In the present study, we elucidate proteomic changes of primary intestinal epithelial cells from jejunum during early suckling (1-7 days of age), middle suckling (7-14 days), and weaning period (14-35 days) in mice, using a label-free proteomics approach. We show differential expression of 520 proteins during intestinal development and a pronounced change of the proteome during the middle suckling period and weaning. Proteins involved in several metabolic processes were found differentially expressed along the development. The temporal expression profiles of enzymes of the glycolysis were found to correlate with the increase in carbohydrate uptake at weaning, whereas the abundance changes of proteins involved in fatty acid metabolism as well as lactose metabolism indicated a nondiet driven preparation for the nutritional change at weaning. Further, we report the developmental abundance changes of proteins playing a vital role in the neonatal acquisition of passive immunity. In addition, different isoforms of several proteins were quantified, which may contribute to a better understanding of the roles of the specific isoforms in the small intestine. In summary, we provide a first, time-resolved proteome profile of intestinal epithelial cells along postnatal intestinal development.

Proteomics in nutrition: status quo and outlook for biomarkers and bioactives.

Food and beverages are the only physical matter we take into our body, if we disregard the air we inhale and the drugs we may have to apply. While traditional nutrition research has aimed at providing nutrients to nourish populations and preventing specific nutrient deficiencies, it more recently explores health-related aspects of individual bioactive components as well as entire diets and this at group rather than population level. The new era of nutrition research translates empirical knowledge to evidence-based molecular science. Modern nutrition research focuses on promoting health, preventing or delaying the onset of disease, optimizing performance, and assessing risk. Personalized nutrition is a conceptual analogue to personalized medicine and means adapting food to individual needs. Nutrigenomics and nutrigenetics build the science foundation for understanding human variability in preferences, requirements, and responses to diet and may become the future tools for consumer assessment motivated by personalized nutritional counseling for health maintenance and disease prevention. The scope of this paper is to review the current and future aspects of nutritional proteomics, focusing on the two main outputs: identification of health biomarkers and analysis of food bioactives.

xComb: a cross-linked peptide database approach to protein-protein interaction analysis.

We developed an informatic method to identify tandem mass spectra composed of chemically cross-linked peptides from those of linear peptides and to assign sequence to each of the two unique peptide sequences. For a given set of proteins the key software tool, xComb, combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files. The xComb library of select theoretical cross-linked peptides may then be used as a database that is examined by a standard proteomic search engine to match tandem mass spectral data sets to identify cross-linked peptides. The database search may be conducted against as many as 50 proteins with a number of common proteomic search engines, e.g. Phenyx, Sequest, OMSSA, Mascot and X!Tandem. By searching against a peptide library of linearized, cross-linked peptides, rather than a linearized protein library, search times are decreased and the process is decoupled from any specific search engine. A further benefit of decoupling from the search engine is that protein cross-linking studies may be conducted with readily available informatics tools for which scoring routines already exist within the proteomic community.

Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique.

Protein complexes are the foundation of a majority of cellular processes. Although a large number of protein complexes have been identified through biochemical experiments, the precise molecular details and three-dimensional structures are available for only a small fraction. Chemical cross-linking coupled with mass spectrometry (CXMS) has gained popularity in recent years for characterization of inter- and intraprotein interactions in protein complexes. This perspective provides a comprehensive and critical overview of CXMS strategies employed for structural elucidation of protein complexes. We evaluate the challenges associated with CXMS techniques with special emphasis on data analysis. As sensitivity, mass resolution, mass accuracy and ease of use of mass spectrometers have improved, the complexity of processing and interpreting CXMS data has become the central problem to be addressed. We review here a number of computer programs available to address these problems.