Charge-State-Dependent Collision-Induced Dissociation Behaviors of RNA Oligonucleotides via High-Resolution Mass Spectrometry

Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1^- to 5^-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO^- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.

Accurate Proteoform Identification and Quantitation Using pTop 2.0

The remarkable advancement of top-down proteomics in the past decade is driven by the technological development in separation, mass spectrometry (MS) instrumentation, novel fragmentation, and bioinformatics. However, the accurate identification and quantification of proteoforms, all clearly-defined molecular forms of protein products from a single gene, remain a challenging computational task. This is in part due to the complicated mass spectra from intact proteoforms when compared to those from the digested peptides. Herein, pTop 2.0 is developed to fill in the gap between the large-scale complex top-down MS data and the shortage of high-accuracy bioinformatic tools. Compared with pTop 1.0, the first version, pTop 2.0 concentrates mainly on the identification of the proteoforms with unexpected modifications or a terminal truncation. The quantitation based on isotopic labeling is also a new function, which can be carried out by the convenient and user-friendly "one-key operation," integrated together with the qualitative identifications. The accuracy and running speed of pTop 2.0 is significantly improved on the test data sets. This chapter will introduce the main features, step-by-step running operations, and algorithmic developments of pTop 2.0 in order to push the identification and quantitation of intact proteoforms to a higher-accuracy level in top-down proteomics.

Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially.

Cross-linking mass spectrometry can provide insights into protein structures and interactions but its scope depends on the reactivity of the cross-linker. Here, the authors develop Arg-Arg and Lys-Arg cross-linkers, which provide structural information elusive to the widely used Lys-Lys cross-linkers.

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, ¹⁵N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.

The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.

[Molecular mechanisms and relationship of M2-polarized macrophages with early response in multiple myeloma]

目的

探讨替代活化型巨噬细胞（M2 MΦ）和多发性骨髓瘤（MM）早期治疗反应的关系及其在发病机制中的可能作用。

方法

采用免疫组化法标记240例MM患者骨髓标本中的MΦ；建立体外M2 MΦ诱导培养体系，构建Transwell共培养模型与RPMI 8226和U266细胞共培养，CCK-8法检测M2 MΦ对细胞增殖的影响，流式细胞术检测对地塞米松（1 µ mol/L）诱导骨髓瘤细胞凋亡的影响，ELISA法检测对TNF-α和IL-6表达的影响，real time PCR法检测对趋化因子、血管内皮生长因子（VEGF）及其受体表达的影响。

结果

①依据骨髓组织M2 MΦ浸润程度将患者分为高浸润组（92例）和低浸润组（148例），高浸润组患者早期治疗有效率明显低于低浸润组，差异有统计学意义（23.9%对73.0%，χ²=60.31，P<0.001）。②培养24、36 h，共培养组细胞增殖能力较对照组显著上升：M2 MΦ+RPMI 8226细胞组与对照组比较，P值分别为0.005、0.020；M2 MΦ+U266细胞与对照组比较，P值分别为0.030、0.020。③地塞米松诱导后，共培养组与对照组比较，RPMI 8226细胞凋亡率下降（29.0%对71.0%，t=4.97，P=0.008），U266细胞凋亡率也下降（24.9%对67.7%，t=6.99，P=0.002）。④共培养48 h后，与对照组比较，加入M2 MΦ后可促进RPMI 8226和U266细胞分泌IL-6、TNF-α，促进表达CCL2、CCL3、CCR2、CCR5、VEGFA、VEGFR-1和VEGFR-2。

结论

MM患者骨髓组织M2 MΦ浸润程度和早期治疗反应相关。M2 MΦ通过促进骨髓瘤细胞分泌系列炎症因子、趋化因子和相关受体的表达，从而促进骨髓瘤细胞增殖以及保护骨髓瘤细胞免于凋亡。

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70-85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset.

pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification

The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with ¹⁵N/¹³C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues.

Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.

[Clinical characteristics in gout patients with different body mass index]

Objective: Obesity is one of the risk factors for gout. The aim of the present study was to evaluate clinical characteristics of gout patients with different BMI. Methods: A total of 5 104 patients with gout were enrolled and divided into three groups according to the BMI. The clinical information was collected and relevant biochemical indices were detected. SPSS software was applied for the statistical analyses. Results: There were significant differences in the ratios of gender, regular exercise, hypertension, tophus, renal insufficiency, hyperlipidemia, impaired glucose metabolism, liver dysfunction among the three groups (all P<0.01). The onset age in overweight [45(36, 55) years] and obese subjects [40(31, 50) years] were earlier than that of the normal weight subjects [50(38, 61) years]. Moreover, waist circumstances [103(99, 108) cm and 94 (90, 98) cm vs 87 (82, 91) cm], systolic pressure [130 (120, 145) mmHg (1 mmHg=0.133 kPa)and 130(120, 140)mmHg vs 128(115, 140) mmHg], diastolic pressure [90 (80, 100) mmHg and 85 (80, 92) mmHg vs 80 (79, 90) mmHg], fasting blood glucose [5.77 (5.30, 6.44) mmol/L and 5.65 (5.19, 6.26) mmol/L vs 5.55 (5.10, 6.15) mmol/L], TG [2.10 (1.46, 3.04) mmol/L and 1.88 (1.35, 2.78) mmol/L vs 1.52 (1.07, 2.39) mmol/L], TC [5.20 (4.55, 5.93) mmol/L and 5.07 (4.46, 5.75) mmol/L vs 4.95 (4.27, 5.65) mmol/L], serum uric acid [483(418, 552) μmol/L and 461(395, 524) μmol/L vs 440 (368, 517) μmol/L], ALT [30 (21, 46) U/L and 25 (18, 36) U/L vs 21 (14, 29) U/L], AST [21(17, 28) U/L and 20 (17, 26) U/L vs 20 (6, 25) U/L], the number of joints involved [2(1, 3)joints and 2(1, 2) joints vs 1(1, 2) joints] in the overweight and obese groups were higher than those in the normal weight group ( all P<0.01). There were no statistical differences in family history, involvement of upper limb joints, kidney stones and coronary heart disease among the three groups (all P>0.05). Conclusions: Obesity is associated with an earlier age of gout onset.With the increase of BMI, the blood pressures, glucose, lipid, serum uric acid, liver transaminase levels and the number of involved joints increased gradually. Cautions should be taken in treating patients with different BMI.

Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications

De novo peptide sequencing has improved remarkably, but sequencing full-length peptides with unexpected modifications is still a challenging problem. Here we present an open de novo sequencing tool, Open-pNovo, for de novo sequencing of peptides with arbitrary types of modifications. Although the search space increases by ∼300 times, Open-pNovo is close to or even ∼10-times faster than the other three proposed algorithms. Furthermore, considering top-1 candidates on three MS/MS data sets, Open-pNovo can recall over 90% of the results obtained by any one traditional algorithm and report 5-87% more peptides, including 14-250% more modified peptides. On a high-quality simulated data set, ∼85% peptides with arbitrary modifications can be recalled by Open-pNovo, while hardly any results can be recalled by others. In summary, Open-pNovo is an excellent tool for open de novo sequencing and has great potential for discovering unexpected modifications in the real biological applications.

[Intratympatic budesonide injection for treatment of refractorysudden sensorineural hearing loss]

Objective:To investigate intratympanic steroid injection for treatment of sudden sensorineural hearing loss after failure of initial systemic therapy,and discuss the role of steroid in refractory sudden sensorineural hearing loss.Method:We included 90 patients who did not response to initial systemic therapy of sudden hearing loss.This research adopted the randomized,controlled trial of clinical research.Ninety qualified patients were divided into 3 groups,30 for each group,intratympanic budesonide for experimental group,dexamethasone for control group-1 while control group-2 did not take intratympanic steroid injection but continue another round of systemic therapy.Intratympanic injection was performed 3 times a week and last for 2 weeks.Alprostadil,mecobalamin,ginkgo biloba extract injection,PNS injection and intravenous hyperbaric oxygen fluid were used for consecutive 10 days in the control group-2.Pure tone audiometry and speech Discrimination Score was retaken at the end of each therapy.Result:The results show that the average PTA of damaged frequencies improved more than 10 dB was considered significant,we had 26.7%(8/30) patients meet this criteria in experiment group,30.0%(9/30) in the control group-1 and 6.7%(2/30) in the control group-2.And the recovery rate between these 3 groups is statistically significant(P<0.05),the average PTA improvement in the experimental group,control group-1 and control-2 was(5.0±11.1)dB,(4.2±12.5)dB and (0±3.33)dB respectively,P<0.05,control group-2 was significantly different from control group-1 and experimental group.The Speech Discrimination Score improvement rates in the experimental group,control group-1 and control-2 was 16.7%,12.0% and 4.2% respectively,but the difference in those 3 groups was not significant.Conclusion:Budesonide intratympanic injection is a save method in treating refractory sudden hearing loss ,and it is as effective as dexamethasone.Intratympanic steroids could be an option for refractory sudden sensorineural hearing loss patients.

Molecular identification and genetic variation of varieties of Styphnolobium japonicum (Fabaceae) using SRAP markers

Thirty-four Styphnolobium japonicum varieties were analyzed using sequence-related amplified polymorphism (SRAP) markers, to investigate genetic variation and test the effectiveness of SRAP markers in DNA fingerprint establishment. Twelve primer pairs were selected from 120 primer combinations for their reproducibility and high polymorphism. We found a total of 430 amplified fragments, of which 415 fragments were considered polymorphic with an average of 34.58 polymorphic fragments for each primer combination. The percentage of polymorphic fragments was 96.60%, and four primer pairs showed 100% polymorphism. Moreover, simple matched coefficients ranged between 0.68 and 0.89, with an average of 0.785, indicating that the genetic variation among varieties was relatively low. This could be because of the narrow genetic basis of the selected breeding material. Based on the similarity coefficient value of 0.76, the varieties were divided into four major groups. In addition, abundant and clear SRAP fingerprints were obtained and could be used to establish DNA fingerprints. In the DNA fingerprints, each variety had its unique pattern that could be easily distinguished from others. The results demonstrated that 34 varieties of S. japonicum had a relatively narrow genetic variation. Hence, a broadening of the genetic basis of breeding material is necessary. We conclude that establishment of DNA fingerprint is feasible by means of SRAP markers.

pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3

Confident characterization of the microheterogeneity of protein glycosylation through identification of intact glycopeptides remains one of the toughest analytical challenges for glycoproteomics. Recently proposed mass spectrometry (MS)-based methods still have some defects such as lack of the false discovery rate (FDR) analysis for the glycan identification and lack of sufficient fragmentation information for the peptide identification. Here we proposed pGlyco, a novel pipeline for the identification of intact glycopeptides by using complementary MS techniques: 1) HCD-MS/MS followed by product-dependent CID-MS/MS was used to provide complementary fragments to identify the glycans, and a novel target-decoy method was developed to estimate the false discovery rate of the glycan identification; 2) data-dependent acquisition of MS3 for some most intense peaks of HCD-MS/MS was used to provide fragments to identify the peptide backbones. By integrating HCD-MS/MS, CID-MS/MS and MS3, intact glycopeptides could be confidently identified. With pGlyco, a standard glycoprotein mixture was analyzed in the Orbitrap Fusion, and 309 non-redundant intact glycopeptides were identified with detailed spectral information of both glycans and peptides.

Field homogeneity improvement of maglev NdFeB magnetic rails from joints

An ideal magnetic rail should provide a homogeneous magnetic field along the longitudinal direction to guarantee the reliable friction-free operation of high temperature superconducting (HTS) maglev vehicles. But in reality, magnetic field inhomogeneity may occur due to lots of reasons; the joint gap is the most direct one. Joint gaps inevitably exist between adjacent segments and influence the longitudinal magnetic field homogeneity above the rail since any magnetic rails are consisting of many permanent magnet segments. To improve the running performance of maglev systems, two new rail joints are proposed based on the normal rail joint, which are named as mitered rail joint and overlapped rail joint. It is found that the overlapped rail joint has a better effect to provide a competitive homogeneous magnetic field. And the further structure optimization has been done to ensure maglev vehicle operation as stable as possible when passing through those joint gaps. The results show that the overlapped rail joint with optimal parameters can significantly reduce the magnetic field inhomogeneity comparing with the other two rail joints. In addition, an appropriate gap was suggested when balancing the thermal expansion of magnets and homogenous magnetic field, which is considered valuable references for the future design of the magnetic rails.

Reprint of "pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data"

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.This article is part of a Special Issue entitled: Computational Proteomics.

pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested.

Using pLink to Analyze Cross-Linked Peptides

pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink.

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture

The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community's ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring modifications combined with a yeast whole cell lysate as background was distributed to a large group of researchers and their results were collectively analyzed. The results from the twenty-four participants, who represented a broad spectrum of experience levels with this type of data analysis, produced several important observations. First, there is significantly more variability in the ability to assess whether a results is significant than there is to determine the correct answer. Second, labile post-translational modifications, particularly tyrosine sulfation, present a challenge for most researchers. Finally, for modification site localization there are many tools being employed, but researchers are currently unsure of the reliability of the results these programs are producing.

DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data

Identification of proteins and their modifications via liquid chromatography-tandem mass spectrometry is an important task for the field of proteomics. However, because of the complexity of tandem mass spectra, the majority of the spectra cannot be identified. The presence of unanticipated protein modifications is among the major reasons for the low spectral identification rate. The conventional database search approach to protein identification has inherent difficulties in comprehensive detection of protein modifications. In recent years, increasing efforts have been devoted to developing unrestrictive approaches to modification identification, but they often suffer from their lack of speed. This paper presents a statistical algorithm named DeltAMT (Delta Accurate Mass and Time) for fast detection of abundant protein modifications from tandem mass spectra with high-accuracy precursor masses. The algorithm is based on the fact that the modified and unmodified versions of a peptide are usually present simultaneously in a sample and their spectra are correlated with each other in precursor masses and retention times. By representing each pair of spectra as a delta mass and time vector, bivariate Gaussian mixture models are used to detect modification-related spectral pairs. Unlike previous approaches to unrestrictive modification identification that mainly rely upon the fragment information and the mass dimension in liquid chromatography-tandem mass spectrometry, the proposed algorithm makes the most of precursor information. Thus, it is highly efficient while being accurate and sensitive. On two published data sets, the algorithm effectively detected various modifications and other interesting events, yielding deep insights into the data. Based on these discoveries, the spectral identification rates were significantly increased and many modified peptides were identified.

Simultaneous structural identification of natural products in fractions of crude extract of the rare endangered plant Anoectochilus roxburghii using H NMR/RRLC-MS parallel dynamic spectroscopy

Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to ¹H NMR and rapid resolution liquid chromatography-mass spectroscopy (RRLC-MS) data, acquired from the crude extract of Anoectochilus roxburghii, which was separated into a series of fractions with the concentration of constituent dynamic variation using reversed-phase preparative chromatography. Through fraction ranges and intensity changing profiles in ¹H NMR/RRLC–MS PDS spectrum, ¹H NMR and the extracted ion chromatogram (XIC) signals deriving from the same individual constituent, were correlated due to the signal amplitude co-variation resulting from the concentration variation of constituents in a series of incompletely separated fractions. 1H NMR/RRLC-MS PDS was then successfully used to identify three types of natural products, including eight flavonoids, four organic acids and p-hydroxybenzaldehyde, five of which have not previously been reported in Anoectochilus roxburghii. In addition, two groups of co-eluted compounds were successfully identified. The results prove that this approach should be of benefit in the unequivocal structural determination of a variety of classes of compounds from extremely complex mixtures, such as herbs and biological samples, which will lead to improved efficiency in the identification of new potential lead compounds.

Speeding up tandem mass spectrometry-based database searching by longest common prefix

Background

Tandem mass spectrometry-based database searching has become an important technology for peptide and protein identification. One of the key challenges in database searching is the remarkable increase in computational demand, brought about by the expansion of protein databases, semi- or non-specific enzymatic digestion, post-translational modifications and other factors. Some software tools choose peptide indexing to accelerate processing. However, peptide indexing requires a large amount of time and space for construction, especially for the non-specific digestion. Additionally, it is not flexible to use.

Results

We developed an algorithm based on the longest common prefix (ABLCP) to efficiently organize a protein sequence database. The longest common prefix is a data structure that is always coupled to the suffix array. It eliminates redundant candidate peptides in databases and reduces the corresponding peptide-spectrum matching times, thereby decreasing the identification time. This algorithm is based on the property of the longest common prefix. Even enzymatic digestion poses a challenge to this property, but some adjustments can be made to this algorithm to ensure that no candidate peptides are omitted. Compared with peptide indexing, ABLCP requires much less time and space for construction and is subject to fewer restrictions.

Conclusions

The ABLCP algorithm can help to improve data analysis efficiency. A software tool implementing this algorithm is available at http://pfind.ict.ac.cn/pfind2dot5/index.htm

Improved peptide identification for proteomic analysis based on comprehensive characterization of electron transfer dissociation spectra

In recent years, electron transfer dissociation (ETD) has enjoyed widespread applications from sequencing of peptides with or without post-translational modifications to top-down analysis of intact proteins. However, peptide identification rates from ETD spectra compare poorly with those from collision induced dissociation (CID) spectra, especially for doubly charged precursors. This is in part due to an insufficient understanding of the characteristics of ETD and consequently a failure of database search engines to make use of the rich information contained in the ETD spectra. In this study, we statistically characterized ETD fragmentation patterns from a collection of 461 440 spectra and subsequently implemented our findings into pFind, a database search engine developed earlier for CID data. From ETD spectra of doubly charged precursors, pFind 2.1 identified 63-122% more unique peptides than Mascot 2.2 under the same 1% false discovery rate. For higher charged peptides as well as phosphopeptides, pFind 2.1 also consistently obtained more identifications. Of the features built into pFind 2.1, the following two greatly enhanced its performance: (1) refined automatic detection and removal of high-intensity peaks belonging to the precursor, charge-reduced precursor, or related neutral loss species, whose presence often set spectral matching askew; (2) a thorough consideration of hydrogen-rearranged fragment ions such as z + H and c - H for peptide precursors of different charge states. Our study has revealed that different charge states of precursors result in different hydrogen rearrangement patterns. For a fragment ion, its propensity of gaining or losing a hydrogen depends on (1) the ion type (c or z) and (2) the size of the fragment relative to the precursor, and both dependencies are affected by (3) the charge state of the precursor. In addition, we discovered ETD characteristics that are unique for certain types of amino acids (AAs), such as a prominent neutral loss of SCH(2)CONH(2) (90.0014 Da) from z ions with a carbamidomethylated cysteine at the N-terminus and a neutral loss of histidine side chain C(4)N(2)H(5) (81.0453 Da) from precursor ions containing histidine. The comprehensive list of ETD characteristics summarized in this paper should be valuable for automated database search, de novo peptide sequencing, and manual spectral validation.

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

Motivation: Identification of post-translationally modified proteins has become one of the central issues of current proteomics. Spectral library search is a new and promising computational approach to mass spectrometry-based protein identification. However, its potential in identification of unanticipated post-translational modifications has rarely been explored. The existing spectral library search tools are designed to match the query spectrum to the reference library spectra with the same peptide mass. Thus, spectra of peptides with unanticipated modifications cannot be identified.

Results: In this article, we present an open spectral library search tool, named pMatch. It extends the existing library search algorithms in at least three aspects to support the identification of unanticipated modifications. First, the spectra in library are optimized with the full peptide sequence information to better tolerate the peptide fragmentation pattern variations caused by some modification(s). Second, a new scoring system is devised, which uses charge-dependent mass shifts for peak matching and combines a probability-based model with the general spectral dot-product for scoring. Third, a target-decoy strategy is used for false discovery rate control. To demonstrate the effectiveness of pMatch, a library search experiment was conducted on a public dataset with over 40 000 spectra in comparison with SpectraST, the most popular library search engine. Additional validations were done on four published datasets including over 150 000 spectra. The results showed that pMatch can effectively identify unanticipated modifications and significantly increase spectral identification rate.

Availability:http://pfind.ict.ac.cn/pmatch/

Contact:yfu@ict.ac.cn; rxsun@ict.ac.cn

Supplementary information:Supplementary data are available at Bioinformatics online.

pNovo: de novo peptide sequencing and identification using HCD spectra

De novo peptide sequencing has improved remarkably in the past decade as a result of better instruments and computational algorithms. However, de novo sequencing can correctly interpret only approximately 30% of high- and medium-quality spectra generated by collision-induced dissociation (CID), which is much less than database search. This is mainly due to incomplete fragmentation and overlap of different ion series in CID spectra. In this study, we show that higher-energy collisional dissociation (HCD) is of great help to de novo sequencing because it produces high mass accuracy tandem mass spectrometry (MS/MS) spectra without the low-mass cutoff associated with CID in ion trap instruments. Besides, abundant internal and immonium ions in the HCD spectra can help differentiate similar peptide sequences. Taking advantage of these characteristics, we developed an algorithm called pNovo for efficient de novo sequencing of peptides from HCD spectra. pNovo gave correct identifications to 80% or more of the HCD spectra identified by database search. The number of correct full-length peptides sequenced by pNovo is comparable with that obtained by database search. A distinct advantage of de novo sequencing is that deamidated peptides and peptides with amino acid mutations can be identified efficiently without extra cost in computation. In summary, implementation of the HCD characteristics makes pNovo an excellent tool for de novo peptide sequencing from HCD spectra.

Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing

Database searching is the technique of choice for shotgun proteomics, and to date much research effort has been spent on improving its effectiveness. However, database searching faces a serious challenge of efficiency, considering the large numbers of mass spectra and the ever fast increase in peptide databases resulting from genome translations, enzymatic digestions, and post-translational modifications. In this study, we conducted systematic research on speeding up database search engines for protein identification and illustrate the key points with the specific design of the pFind 2.1 search engine as a running example. Firstly, by constructing peptide indexes, pFind achieves a speedup of two to three compared with that without peptide indexes. Secondly, by constructing indexes for observed precursor and fragment ions, pFind achieves another speedup of two. As a result, pFind compares very favorably with predominant search engines such as Mascot, SEQUEST and X!Tandem.

pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry

This paper describes the pFind 2.0 software package for peptide and protein identification via tandem mass spectrometry. Firstly, the most important feature of pFind 2.0 is that it offers a modularized and customized platform for third parties to test and compare their algorithms. The developers can create their own modules following the open application programming interface (API) standards and then add it into workflows in place of the default modules. In addition, to accommodate different requirements, the package provides four automated workflows adopting different algorithm modules, executing processes and result reports. Based on this design, pFind 2.0 provides an automated target-decoy database search strategy: The user can just specify a certain false positive rate (FPR) and start searching. Then the system will return the protein identification results automatically filtered by such an estimated FPR. Secondly, pFind 2.0 is also of high accuracy and high speed. Many pragmatic preprocessing, peptide-scoring, validation, and protein inference algorithms have been incorporated. To speed up the searching process, a toolbox for indexing protein databases is developed for high-throughput applications and all modules are implemented under a new architecture designed for large-scale parallel and distributed searching. An experiment on a public dataset shows that pFind 2.0 can identify more peptides than SEQUEST and Mascot at the 1% FPR. It is also demonstrated that this version of pFind 2.0 has better usability and higher speed than its previous versions. The software and more detailed supplementary information can both be accessed at http://pfind.ict.ac.cn/.

Inhibitory effects of synthetic beta peptide on invasion and metastasis of liver cancer

PURPOSE

To study the inhibitory effects of synthetic beta peptide on invasion and metastasis of liver cancer.

METHODS

Membrane-type intercellular adhesion molecule-1 (ICAM-1) expression of SMMC-7721 cultured hepatoma cells (7721 cells) was detected by immunofluorescence cell flowmeter. The adhesion of 7721 cells to fibronectin (FN) was assayed by the MTT method. The adhesion of 7721 cells to 7721 cells, 7721 cells to endothelial cells, and 7721 cells to lymphocyte cells was detected by adhesion assay. LCI-D20 human liver cancer metastasis model in nude mice was used in this experiment. One hundred micrograms of beta peptide per mouse were injected subcutaneously after tumor was resected premetastatically or postmetastatically to observe its effect on liver cancer metastasis after hepatectomy.

RESULTS

Membrane-type ICAM-1 expression of SMMC-7721 cells treated by beta peptide was lower than that of the untreated cells. The adhesion of 7721 cells to FN, 7721 cells to 7721 cells, 7721 cells to endothelial cells, and 7721 cells to lymphocyte cells was also lower in the beta peptide group than in the untreated group.

CONCLUSIONS

beta Peptide can block the adhesion of 7721 cells to FN, 7721 cells to some host cells in vitro, and inhibit HCC metastasis of LCI-D20 model posthepatectomy in vivo, so it could potentially act as an antimetastasis drug.

MBR rearrangement and P-glycoprotein expression are not independent prognostic factors like p53 protein in malignant lymphoma

Non-Hodgkin's lymphomas (NHL) are B-cell malignancies which generally present molecular abnormalities, such as bcl-2 translocation t(14; 18) predominantly in the follicular subgroup. Other molecular events have been described in NHL, including p53 gene mutation and overexpression of one chemoresistance mechanism, the multidrug resistance system, P-glycoprotein (MDR 1/P-gp). In this study, we analysed samples from 44 NHL patients with the presence of the bcl-2 major breakpoint region (MBR) rearrangement in 29 and without in 15. Immunochemical analysis revealed that 39 samples were positive for bcl-2 protein expression in tumoral cells (88.6%). Seventeen (38.6%) patients expressed P-gp and 9 (20.5%) expressed p53 proteins. Eleven patients expressed both bcl-2 and P-gp proteins, four expressed bcl-2 and p53 proteins whereas four expressed bcl-2, p53 and P-gp proteins. Our results confirm the importance of p53 expression as a key prognostic factor, and no objective response (OR) was found in patients with p53 positivity. MBR rearrangement was not associated with poor response to chemotherapy (62.1% OR in MBR positive patients v. 60% OR in MBR negative patients). The clinical impact of P-gp cannot be identified because no relationship was observed between P-gp expression and prognosis (58.8% OR in P-gp positive patients v. 63% OR in P-gp negative patients).

Large scale and clinical grade purification of syndecan-1+ malignant plasma cells

For cancer immunotherapy, it is usually necessary to obtain a large number of tumor cells from patients. We have previously reported that syndecan-I is present only on malignant plasma cells in samples from patients with multiple myelomatosis. We report here that this antigen is cleaved by chymopapain. This makes it possible to develop a rapid and clinical grade procedure to purify large numbers of myeloma cells using anti-syndecan-1 mAb, magnetic beads and chymopapain.

Specific inhibition of IL-6 signalling with monoclonal antibodies against the gp130 receptor

A family of cytokines [IL-6, IL-11, oncostatin M (OM), leukaemia inhibitory factor (LIF), ciliary neurotrophic factor (CNTF) and cardiotrophin-1] involved in various inflammatory or tumoral diseases share the same gp130 signal transducer chain. The complex formed with their specific receptors associates with a common transducing gp130 membrane protein (gp130) resulting in the formation of high avidity receptor and activation of tyrosine kinases. With the view of identifying gp130 domains specifically involved in IL-6 signalling, the authors prepared 37 new anti-gp130 mAb and analysed the structure-function relationship of the molecule. By cross-competition ELISA, the mAb were classified in 10 subgroups called A to J. By ELISA and BIAcore analysis, the mAb were found to recognize at least 18 antigenic specificities of the gp130 chain. The mAb reacted against the soluble and the membrane forms of gp130 as well. Their ability to inhibit the proliferation of the human myeloma cell line XG-4 of which the growth is strictly dependent on the presence of either exogenous IL-6, or LIF, or OM, or CNTF was studied. Besides mAb with no evident neutralizing effect (G and H) and mAb which neutralized equally well the activity of all tested cytokines (all mAb of groups A, I and J), some showed a selective effect. Those of group F inhibited also the proliferation induced by the 4 cytokines, but more specifically that dependent on the CNTF. mAb of groups B and E specifically inhibited the growth induced by IL-6, whereas those of group C inhibited that induced by LIF and OM. These results show the presence of different gp130 epitopes specifically involved in the signaling induced by the cytokines of the gp130 family. In ELISA, only mAb of group B and E were found to inhibit the binding of the IL-6-IL-6R complex to gp130, showing that they identified one or two domains of gp130 involved in its interaction with the IL-6-IL-6R complex. Precise identification of this(ese) epitope(s) would be useful to better understand the mechanisms of the IL-6 signalling.

Interleukin-6 receptor antagonists inhibit interleukin-11 biological activity

The IL-6 receptor system comprises two functionally different chains: a binding chain (IL-6R) and a signal-transducing chain (gp130). The IL-6/IL-6R complexes associate with gp130, induce its dimerization and signal transduction. When IL-6 is complexed to IL-6R, two distinct sites of IL-6 are able to bind gp130. Other cytokines-oncostatin M (OM), leukemia inhibitory factor (LIF) or ciliary neurotrophic factor (CNTF) also use the gp130 transducer and induce its heterodimerization with LIF receptor (LIFR). A series of IL-6 mutants have been generated which function as IL-6 receptor antagonists (IL-6RA). These IL-6RA carried substitutions that increased their affinity with IL-6R and abolished 1 or the 2 sites of interaction with gp130. All the IL-6RA inhibited wild-type IL-6. The IL-6RA with one mutated binding site to gp130 inhibited IL-11 activity. They did not affect those of CNTF, LIF and OM, even when used at a very high concentration at which virtually all membrane IL-6R were bound to IL-6RA. IL-6RA with two mutated gp130 binding sites did not affect IL-11, CNTF, LIF or OM activities. The results indicate that the interaction of one gp130 chain with IL-6R/IL-6R complexes inhibited further the dimerization of gp130 induced by IL-11/IL-11R but not its heterodimerization with LIFR. Thus these IL-6RA can also function as IL-11 antagonists.

A plasmocyte selective monoclonal antibody (B-B4) recognizes syndecan-1

We developed a new monoclonal antibody. B-B4, which specifically identifies human plasma cells. It strongly reacts with all multiple myeloma cell lines and with malignant plasma cells of all tumour samples of the multiple myeloma patients tested. B-B4 does not react with any peripheral blood, bone marrow or tonsil cells. Cloning of the B-B4 antigen reveals that the monoclonal antibody recognizes syndecan-1. It appears that the monoclonal antibody B-B4 is a suitable marker for human plasmocyte identification among haemopoietic cells and a useful probe for the diagnosis of haematological malignancies. Furthermore, this monoclonal antibody can be used for depletions prior to CD34 grafting.

Human interleukin-6 receptor super-antagonists with high potency and wide spectrum on multiple myeloma cells

Interleukin-6 (IL-6) is the major growth factor for myeloma cells and is believed to participate in the pathogenesis of chronic autoimmune diseases and postmenopausal osteoporosis. IL-6 has been recently shown to possess three topologically distinct receptor binding sites: site 1 for binding to the subunit specific chain IL-6R alpha and sites 2 and 3 for the interaction with two subunits of the signaling chain gp130. We have generated a set of IL-6 variants that behave as potent cytokine receptor super-antagonists carrying substitutions that abolish interaction with gp130 at either site 2 alone (site 2 antagonist) or at both sites 2 and 3 (site 2 + 3 antagonist). In addition, substitutions have been introduced in site 1 that lead to variable increases in binding for IL-6R alpha up to 70-fold. IL-6 super-antagonists inhibit wild-type cytokine activity with efficacy proportional to the increase in receptor binding on a variety of human call lines of different origin, and the most potent molecules display full antagonism at low molar excess to wild-type IL-6. When tested on a representative set of IL-6-dependent human myeloma cell lines, although site 2 super-antagonists were in general quite effective, only the site 2 + 3 antagonist Sant7 showed antagonism on the full spectrum of cells tested. In conclusion, IL-6 super-antagonists are a useful tool for the study of myeloma in vitro and might constitute, in particular Sant7, effective IL-6 blocking agents in vivo.