Computational approach to structural identification of phospholipids using raw mass spectra from nanoflow liquid chromatography–electrospray ionization–tandem mass spectrometry

A qualitative analysis tool (LiPilot) for identifying phospholipids (PLs), including lysophospholipids (LPLs), from biological mixtures is introduced. The developed algorithm utilizes raw data obtained from nanoflow liquid chromatography–electrospray ionization–tandem mass spectrometry experiments of lipid mixture samples including retention time and m/z values of precursor and fragment ions from data‐dependent, collision‐induced dissociation. Library files based on typical fragmentation patterns of PLs generated with an LTQ‐Velos ion trap mass spectrometer are used to identify PL or LPL species by comparing experimental fragment ions with typical fragment ions in the library file. Identification is aided by calculating a confidence score developed in our laboratory to maximize identification efficiency. Analysis includes the influence of total ion intensities of matched and unmatched fragment ions, the difference in m/z values between observed and theoretical fragment ions, and a weighting factor used to differentiate regioisomers through data filtration. The present study focused on targeted identification of particular PL classes. The identification software was evaluated using a mixture of 24 PL and LPL standards. The software was further tested with a human urinary PL mixture sample, with 93 PLs and 22 LPLs identified. Copyright © 2012 John Wiley & Sons, Ltd.     

Evaluation of the sensitivity of the ‘Wiley registry of tandem mass spectral data,MSforID’ with MS/MS data of the ‘NIST/NIH/EPA mass spectral library’

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the ‘NIST/NIH/EPA Mass Spectral Library’ (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross‐validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.     

Testing an alternative search algorithm for compound identification with the ‘Wiley Registry of Tandem Mass Spectral Data,MSforID’

A tandem mass spectral database system consists of a library of reference spectra and a search program. State‐of‐the‐art search programs show a high tolerance for variability in compound‐specific fragmentation patterns produced by collision‐induced decomposition and enable sensitive and specific ‘identity search’. In this communication, performance characteristics of two search algorithms combined with the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were evaluated. The search algorithms tested were the MSMS search algorithm implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30 000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their setup from tandem‐in‐space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS. Copyright © 2013 John Wiley & Sons, Ltd.     

MassBank: a public repository for sharing mass spectral data for life sciences

MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron‐ionization mass spectrometry(EI‐MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)‐MSⁿ data of 2337 authentic compounds of metabolites, 11 545 EI‐MS and 834 other‐MS data of 10 286 volatile natural and synthetic compounds, and 3045 ESI‐MS² data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI‐MS² data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass‐to‐charge ratio are optimized to the ESI‐MS² data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI‐MS² data on an identical compound under different collision‐induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21–23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data. Copyright © 2010 John Wiley & Sons, Ltd.     

Fragmentation trees for the structural characterisation of metabolites

Metabolite identification plays a crucial role in the interpretation of metabolomics research results. Due to its sensitivity and widespread implementation, a favourite analytical method used in metabolomics is electrospray mass spectrometry. In this paper, we demonstrate our results in attempting to incorporate the potentials of multistage mass spectrometry into the metabolite identification routine. New software tools were developed and implemented which facilitate the analysis of multistage mass spectra and allow for efficient removal of spectral artefacts. The pre‐processed fragmentation patterns are saved as fragmentation trees. Fragmentation trees are characteristic of molecular structure. We demonstrate the reproducibility and robustness of the acquisition of such trees on a model compound. The specificity of fragmentation trees allows for distinguishing structural isomers, as shown on a pair of isomeric prostaglandins. This approach to the analysis of the multistage mass spectral characterisation of compounds is an important step towards formulating a generic metabolite identification method. Copyright © 2012 John Wiley & Sons, Ltd.     

On the inter‐instrument and the inter‐laboratory transferability of a tandem mass spectral reference library. 3. Focus on ion trap and upfront CID

Mass spectral libraries represent versatile tools for the identification of small bioorganic molecules. Libraries based on electron impact spectra are rated robust and transferable. Tandem mass spectral libraries are often considered to work properly only on the instrument that has been used to build the library. An exception from that rule is the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’. In various studies with data sets from different kinds of tandem mass spectrometric instruments, the outstanding sensitivity and robustness of this tandem mass spectral library search approach was demonstrated. The instrumental platforms tested, however, mainly included various tandem‐in‐space instruments. Herein, the results of a multicenter study with a focus on upfront and tandem‐in‐time fragmentation are presented. Five laboratories participated and provided fragment ion mass spectra from the following types of mass spectrometers: time‐of‐flight (TOF), quadrupole–hexapole–TOF, linear ion trap (LIT), 3‐D ion trap and LIT–Orbitrap. A total number of 1231 fragment ion mass spectra were collected from 20 test compounds (amiloride, buphenin, cinchocaine, cyclizine, desipramine, dihydroergotamine, dyxirazine, dosulepin, ergotamine, ethambutol, etofylline, mefruside, metoclopramide, phenazone, phentermine, phenytoin, sulfamethoxazole, sulfamoxole, sulthiame and tetracycline) on seven electrospray ionization instruments using 18 different instrumental configurations for fragmentation. For 1222 spectra (99.3%), the correct compound was retrieved as the best matching compound. Classified matches (matches with ‘relative average match probability’ >40.0) were obtained for 1207 spectra (98.1%). This high percentage of correct identifications clearly supports the hypothesis that the tandem mass spectral library approach tested is a robust and universal identification tool. Copyright © 2012 John Wiley & Sons, Ltd.     

Rapid LC‐MS‐based metabolomics method to study the Fusarium infection of barley

Ultra high performance liquid chromatography with quadrupole/time‐of‐flight mass spectrometry was applied to evaluate the potential of nontarget metabolomic fingerprinting in order to distinguish Fusarium‐infected and control barley samples. First, the sample extraction and instrumental conditions were optimized to obtain the broadest possible representation of polar/medium‐polar compounds occurring in extracts obtained from barley grain samples. Next, metabolomic fingerprints of extracts obtained from nine barley varieties were acquired under ESI conditions in both positive and negative mode. Each variety of barley was tested in two variants: artificially infected by Fusarium culmorum at the beginning of heading and a control group (no infection). In addition, the dynamics of barley infection development was monitored using this approach. The experimental data were statistically evaluated by principal component analysis, hierarchical clustering analysis, and orthogonal partial least‐squares discriminant analysis. The differentiation of barley in response to F. culmorum infection was feasible using this metabolomics‐based method. Analysis in positive mode provided a higher number of molecular features as compared to that performed under negative mode setting. However, the analysis in negative mode permitted the detection of deoxynivalenol and deoxynivalenol‐3‐glucoside considered as resistance‐indicator metabolites in barley.     

Rapid characterization of chlorogenic acids in Duhaldea nervosa based on ultra‐high‐performance liquid chromatography–linear trap quadropole‐Orbitrap‐mass spectrometry and mass spectral trees similarity filter technique

Duhaldea nervosa (Wallich ex Candolle) A. Anderberg has been traditionally used as a food spice and also in folk medicine for treating traumatic injury and relieving rheumatism, especially accelerating the healing of a fracture. However, so far as we are aware, the chemical constituents have not been fully investigated. In this study, a practical method of mass spectral trees similarity filter, a data‐mining technique, was developed and evaluated for the rapid detection and identification complicated constituents based on ultra‐high‐performance liquid chromatography–linear trap quadropole‐Orbitrap‐mass spectrometry. Finally, a total of 47 chlorogenic acids, including 19 monoacyl‐quinic acids, 22 diacyl‐quinic acids, and six triacyl‐quinic acids, were unambiguously or tentatively identified based on their accurate mass measurement, chromatographic retention, MSⁿ spectra, and bibliography data. To our best knowledge, it is the first time to report the chlorogenic acids of D. nervosa, which would be beneficial for the further material basis and quality research. Meanwhile, this mass spectral trees similarity filter method could be envisioned to exhibit a wide application for the identification of complicated components from botanical extracts.     

Towards a universal LC–MS screening procedure – can an LIT LC–MSn screening approach and reference library be used on a quadrupole‐LIT hybrid instrument?

In contrast to libraries with highly reproducible gas chromatography electron ionization mass spectra, current liquid chromatography (LC–MS) libraries are limited to specific instrument types. Therefore, the aim of the study was to prove whether a recently developed linear ion trap (LIT) LC–MSⁿ screening approach and reference library can be transferred to an LC–MS/MS system with a quadrupole‐LIT hybrid mass analyzer using SmileMS, a sophisticated search algorithm. The LIT reference library was built with MS² and MS³ wideband spectra recorded on a ThermoFisher LXQ LIT with electrospray ionization in positive mode and full‐scan data‐dependent acquisition (DDA). Collision parameter optimizations, including different scan types and energies, were performed on an Applied Biosystems QTRAP 4000 system using electrospray ionization in positive mode and full‐scan DDA. Modified library sets were generated to improve the detection of a compound by the used search algorithm. Additionally, 100 authentic human urine samples were screened by both systems for proof of applicability. In the applicability study, 533 compounds were detected by the LXQ and 477 by the QTRAP system using enhanced product ion scan and a modified database. The presented data showed that the LIT screening approach and reference library could be used successfully on a QTRAP instrument with some limitations. These should be overcome by further optimizations regarding DDA settings for better sensitivity and further library modifications to reduce spectra mismatches. Copyright © 2012 John Wiley & Sons, Ltd.     

An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data

A method is presented for extracting individual component spectra from gas chromatography/mass spectrometry (GC/MS) data files and then using these spectra to identify target compounds by matching spectra in a reference library. It extends a published “model peak” approach which uses selected ion chromatograms as models for component shape. On the basis of this shape, individual mass spectral peak abundance profiles are extracted to produce a “purified” spectrum. In the present work, ion-counting noise is explicitly treated and a number of characteristic features of GC/MS data are taken into account. This allows spectrum extraction to be reliably performed down to very low signal levels and for overlapping components. A spectrum match factor for compound identification is developed that incorporates a number of new corrections, some of which employ information derived from chromatographic behavior. Test results suggest that the ability of this system to identify compounds is comparable to that of conventional analysis.     

On the inter‐instrument and inter‐laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study

The inter‐instrument and inter‐laboratory transferability of a tandem mass spectral reference library originally built on a quadrupole‐quadrupole‐time‐of‐flight instrument was examined. The library consisted of 3759 MS/MS spectra collected from 402 reference compounds applying several different collision‐energy values for fragmentation. In the course of the multicenter study, 22 test compounds were sent to three different laboratories, where 418 tandem mass spectra were acquired using four different instruments from two manufacturers. The study covered the following types of tandem mass spectrometers: quadrupole‐quadrupole‐time‐of‐flight, quadrupole‐quadrupole‐linear ion trap, quadrupole‐quadrupole‐quadrupole, and linear ion trap‐Fourier transform ion cyclotron resonance mass spectrometer. In each participating laboratory, optimized instrumental parameters were gathered solely from routinely applied workflows. No standardization procedure was applied to increase the inter‐instrument comparability of MS/MS spectra. The acquired tandem mass spectra were matched against the established reference library using a sophisticated matching algorithm, which is presented in detail in a companion paper. Correct answers, meaning that the correct compound was retrieved as top hit, were obtained in 98.1% of cases. For the remaining 1.9% of spectra, the correct compound was matched at second rank. The observed high percentage of correct assignments clearly suggests that the developed mass spectral library search approach is to a large extent platform independent. Copyright © 2009 John Wiley & Sons, Ltd.     

Metabolomics‐based parallel discovery of xenobiotics and induced endogenous metabolic dysregulation in clinical toxicology

Intoxication by xenobiotics triggers the perturbation of metabolic fingerprints in biofluids, including the accumulation of xenobiotic compounds and the dysregulation of endogenous metabolites. In this work, an untargeted metabolomics workflow was developed to simultaneously profile both xenobiotic and endogenous metabolites for the identification of the xenobiotic origin and an in‐depth understanding of the intoxication mechanism. This workflow was demonstrated in a real‐world clinical case. Plasma samples were collected from four intoxicated children and another three healthy children. Untargeted metabolomics analysis was performed using ultraperformance liquid chromatography (UPLC) coupled to a high‐resolution mass spectrometer (HRMS) with data‐independent MS^E acquisition. LC–MS^E data was processed using an untargeted metabolomics data interpretation workflow, in which the identities of xenobiotics and altered endogenous metabolic features were determined via database searching. Five xenobiotic chemicals and 19 endogenous metabolites were found to be dysregulated. Combined with the clinical evidence, penfluridol was confirmed as the xenobiotic toxin. Furthermore, a mechanistic hypothesis was developed to explain the dysregulation of the four endogenous acyl‐carnitines. This workflow can be readily applied to a wide range of clinical toxicology cases, offering a powerful and convenient means of simultaneous discovery of intoxication source and the understanding of intoxication mechanisms.     

Comparison of MALDI‐TOF mass spectra with microsatellite length polymorphisms in Candida albicans

Candida albicans is the most frequent yeast involved in human infections. Its population structure can be divided into several genetic clades, some of which have been associated with antifungal susceptibility. Therefore, detecting and monitoring fungal clones in a routine laboratory setting would be a major epidemiological advance. Matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectra results are now widely used as bar codes to identify microorganisms in clinical microbiology laboratories. This study aimed at testing MALDI‐TOF mass spectra bar codes to identify clades among a set of C. albicans isolates. Accordingly, 102 clinical strains were genotyped using 10 microsatellite markers and analyzed via MALDI‐TOF mass spectrometry. The mass spectra were compared with a reference spectral library including 33 well‐characterized collection strains, using a Microflex^TM system and Biotyper^TM software, to test the capacity of the spectrum of a given isolate to match with the reference mass spectrum of an isolate from the same genetic clade. Despite high confidence species identification, the spectra failed to significantly match with the corresponding clade (p = 0.74). This was confirmed with the MALDI‐TOF spectra similarity dendrogram, in which the strains were dispersed irrespective of their genetic clade. Various attempts to improve intra‐clade spectra recognition were unsuccessful. In conclusion, MALDI‐TOF mass spectra bar code analysis failed to reliably recognize genetically related C. albicans isolates. Further studies are warranted to develop alternative MALDI‐TOF mass spectra analytical approaches to identify and monitor C. albicans clades in the routine clinical laboratory. Copyright © 2015 John Wiley & Sons, Ltd.     

On the risk of false positive identification using multiple ion monitoring in qualitative mass spectrometry: Large-scale intercomparisons with a comprehensive mass spectral library

Analysts involved in qualitative mass spectrometry have long debated the minimum data requirements for demonstrating that signals from an unknown sample are identical to those from a known compound. Often this process is carried out by comparing a few selected ions acquired by multiple ion monitoring (MIM), with due allowance for expected variability in response. In a few past experiments with electron-ionization mass spectrometry (EI-MS), the number of ions selected and the allowable variability in relative abundance were tested by comparing one spectrum against a library of mass spectra, where library spectra served to represent potential false positive signals in an analysis. We extended these experiments by carrying out large-scale intercomparisons between thousands of spectra and a library of one hundred thousand EI mass spectra. The results were analyzed to gain insights into the identification confidence associated with various numbers of selected ions. A new parameter was investigated for the first time, to take into account that a library spectrum with a different base peak than the search spectrum may still cause a false positive identification. The influence of peak correlation among the specific ions in all the library mass spectra was also studied. Our computations showed that (1) false positive identifications can result from similar compounds, or low-abundance peaks in unrelated compounds if the method calls for detection at very low levels; (2) a MIM method's identification confidence improves in a roughly continuous manner as more ions are monitored, about one order of magnitude for each additional ion selected; (3) full scan spectra still represent the best alternative, if instrument sensitivity is adequate. The use of large scale intercomparisons with a comprehensive library is the only way to provide direct evidence in support of these conclusions, which otherwise depend on the judgment and experience of individual analysts. There are implications for residue chemists who would rely on standardized confirmation criteria to assess the validity of a given confirmatory method. For example, standardized confirmation criteria should not be used in the absence of interference testing and rational selection of diagnostic ions.     

应用非同质荷比规则提高蛋白质组学检索结果的可信度和灵敏度

如何筛选合理的数据库匹配结果对于基于质谱的蛋白质组学研究至关重要。但是目前,基于打分体系和反转数据库的筛选方法都无法有效的避免假阳性和假阴性匹配的存在。因此,本文提出了一种系统的搜索策略: 非同质荷比检索规则 (INMZS)。在该策略中,所有匹配结果都需要检查相关匹配质荷比的分享程度,只有那些相关质荷比均为专有匹配时,蛋白质才会被作为可信结果保留,策略还采用迭代搜索方法以提高鉴定低丰度组分的灵敏度。最终,所有的匹配结果由诱饵数据库方法进行评估以得到最终结果列表。INMZS策略在标准蛋白质混合物和大规模人肝蛋白质组数据上进行了模拟及应用,结果显示,INMZS规则和诱饵数据库评估方法的结和可以有效的保证蛋白质组学数据匹配的可信度及灵敏度,可以广泛适用于基于二维凝胶电泳及非shotgun技术的蛋白组学研究中。     

True ion pick (TIPick): a denoising and peak picking algorithm to extract ion signals from liquid chromatography/mass spectrometry data

Liquid Chromatography ‐ Time of Flight Mass Spectrometry has become an important technique for toxicological screening and metabolomics. We describe TIPick a novel algorithm that accurately and sensitively detects target compounds in biological samples. TIPick comprises two main steps: background subtraction and peak picking. By subtracting a blank chromatogram, TIPick eliminates chemical signals of blank injections and reduces false positive results. TIPick detects peaks by calculating the S(CC_INI) values of extracted ion chromatograms (EICs) without considering peak shapes, and it is able to detect tailing and fronting peaks. TIPick also uses duplicate injections to enhance the signals of the peaks and thus improve the peak detection power. Commonly seen split peaks caused by either saturation of the mass spectrometer detector or a mathematical background subtraction algorithm can be resolved by adjusting the mass error tolerance of the EICs and by comparing the EICs before and after background subtraction. The performance of TIPick was tested in a data set containing 297 standard mixtures; the recall, precision and F‐score were 0.99, 0.97 and 0.98, respectively. TIPick was successfully used to construct and analyze the NTU MetaCore metabolomics chemical standards library, and it was applied for toxicological screening and metabolomics studies. Copyright © 2013 John Wiley & Sons, Ltd.     

A quantitative LC–MS/MS method for determination of a small molecule agonist of EphA2 in mouse plasma and brain tissue

Compound 27 {1, 12‐bis[4‐(4‐amino‐6,7‐dimethoxyquinazolin‐2‐yl)piperazin‐1‐yl]dodecane‐1,12‐dione} is a novel small molecule agonist of EphA2 receptor tyrosine kinase. It showed much improved activity for the activation of EphA2 receptor compared with the parental compound doxazosin. To support further pharmacological and toxicological studies of the compound, a method using liquid chromatography and electrospray ionization tandem mass spectrometry (LC–MS/MS) has been developed for the quantification of this compound. Liquid–liquid extraction was used to extract the compound from mouse plasma and brain tissue homogenate. Reverse‐phase chromatography with gradient elution was performed to separate compound 27 from the endogenous molecules in the matrix, followed by MS detection using positive ion multiple reaction monitoring mode. Multiple reaction monitoring transitions m/z 387.3 → 290.1 and m/z 384.1 → 247.1 were selected for monitoring compound 27 and internal standard prazosin, respectively. The linear calibration range was 2–200 ng/mL with the intra‐ and inter‐day precision and accuracy within the acceptable range. This method was successfully applied to the quantitative analysis of compound 27 in mouse plasma and brain tissue with different drug administration routes.     

Chemical profiling by LC–MS/MS and HPLC fingerprint combined with chemometrics and simultaneous determination of 16 characteristic ingredients for the quality consistency evaluation of Shaoyao‐Gancao Decoction

In this paper, to evaluate the effect of the region of origin on the quality consistency of Shaoyao‐Gancao Decoction (SGD), the SGD fingerprint was developed for the first time. Chemometric methods including similarity analysis, hierarchical clustering analysis and principal component analysis were employed to study the quality consistency of SGD. Meanwhile, high‐performance liquid chromatography coupled with electrospray ionization quadrupole time‐of‐flight mass spectrometry was applied for comprehensive analysis of SGD and 93 compounds were tentatively characterized. Furthermore, a high‐performance liquid chromatography method with multi‐wavelength switching for simultaneous determination of 16 characteristic ingredients comprising gallic acid, oxypaeniflorin, albiflorin, paeoniflorin, liquiritin apioside, liquiritin, isoliquiritin apioside, galloylpaeoniflorin, 1,2,3,4,6‐penta‐O‐galloyl‐d ‐galactopyranose (PGG), ononin, isoliquiritin, liquiritigenin, benzoylpaeoniflorin, glycyrrhizic acid, isoliquiritigenin and formononetin, was established. All 16 analytes show excellent linearity (R² ≥ 0.9990) with recoveries ranging from 96.58 to 104.61% and limits of detection and quantification of 0.022–0.291 and 0.037–0.635 μg/mL, respectively. Finally, it was successfully applied to determine 15 batches of SGD. The results of our research indicate that different regions of origin have a significant effect on the quality consistency of SGD, and its fingerprint combined with chemometrics and multi‐ingredient determination comprise an efficient and reliable approach for quality consistency evaluation.     

Fast Epitope Mapping for the Anti‐MUC1 Monoclonal Antibody by Combining a One‐Bead‐One‐Glycopeptide Library and a Microarray Platform

Anti‐MUC1 monoclonal antibodies (mAbs) are powerful tools that can be used to recognize cancer‐related MUC1 molecules, the O‐glycosylation status of which is believed to affect binding affinity. We demonstrate the feasibility of using a rapid screening methodology to elucidate those effects. The approach involves i) “one‐bead‐one‐compound”‐based preparation of bilayer resins carrying glycopeptides on the shell and mass‐tag tripeptides coding O‐glycan patterns in the core, ii) on‐resin screening with an anti‐MUC1 mAb, iii) separating positive resins by utilizing secondary antibody conjugation with magnetic beads, and (iv) decoding the mass‐tag that is detached from the positive resins pool by using mass spectrometric analysis. We tested a small library consisting of 27 MUC1 glycopeptides with different O‐glycosylations against anti‐MUC1 mAb clone VU‐3C6. Qualitative mass‐tag analysis showed that increasing the number of glycans leads to an increase in the binding affinity. Six glycopeptides selected from the library were validated by using a microarray‐based assay. Our screening provides valuable information on O‐glycosylations of epitopes leading to high affinity with mAb.