Peptide sequencing by tandem mass spectrometry. Medical search. Frequent questions

Use of the support vector machine and these additional parameters resulted in a more accurate interpretation of peptide MS/MS spectra, and is an important step towards automated interpretation of peptide tandem mass spectrometry data in proteomics. (washington.edu)
Proteomics relies mainly on mass spectrometry. (proprofs.com)
Mass spectrometry is a powerful technique used in proteomics to analyze and measure the mass of proteins. (proprofs.com)
The studies presented here have applied modern analytical proteomics methodologies (in particular, multiplexed tandem mass spectrometry) to characterize the conjugation chemistry of industrially relevant diisocyanates on model proteins. (cdc.gov)
2018. Sequencing Grade Tandem Mass Spectrometry for Top-Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer. . (oregonstate.edu)
Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering the utility of proteomics in applications where the sequences are unknown including variant calling, neoepitope identification, and metaproteomics. (biorxiv.org)
Characterization and identification of microorganisms, using, bottom-up proteomics, or "proteotyping", relies on recognition of species-unique or associated peptides, by tandem mass spectrometry analyses, dependent upon an accurate and comprehensive foundation of genome sequence data, allowing for differentiation of species, at amino acid-level resolution. (chalmers.se)
Water chromatography in conjunction with tandem mass spectrometry has revolutionized the proteomics evaluation of complexes tissue and cells. (cancer-ecosystem.com)
Using proteomics data produced on various kinds of mass spectrometers we optimized the De-Noise algorithm predicated on the quality and mass precision from the mass spectrometer used in the LC/MS/MS test. (cancer-ecosystem.com)
Importantly, mass spectrometry is a key technique in the expanding field of proteomics. (esotech.org)
Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the whole proteome-scale. (biorxiv.org)
Mass spectrometry-based proteomics now enables genome-scale measurements of proteomes from diverse cells, tissues, and organisms. (biorxiv.org)
Stable Isotope Products for Chemical Labeling Stable isotope coded chemical tags enable researchers to perform mass spectrometric- based proteomics studies in the absence of metabolic labeling. (firebaseapp.com)
In proteomics, high throughput approaches using mass spectrometry have be- come widely used. (lu.se)
The need to keep track of protein modifications is readily recognized by the proteomics community, and few repositories of known peptide modifications have been created. (lu.se)

A set of tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. (bioconductor.org)
TURE(default) remove shared peptides by information of # Proteins column in PSM sheet. (bioconductor.org)
TRUE(default) removes peptides that are assigned for more than one proteins. (bioconductor.org)
TRUE will remove the proteins which have only 1 peptide and charge. (bioconductor.org)
Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. (nature.com)
We used consecutive orthogonal separation platforms to ensure sensitive detection: (a) ion-exchange of intact proteins, (b) SDS-PAGE separation of ion-exchange fractions and (c) HPLC separation of tryptic digests coupled to electrospray tandem mass spectrometry. (hindawi.com)
Following activation by agonists such as thrombin, platelets release storage granules and membrane vesicles that contain prothrombotic (e.g., fibrinogen), mitogenic (e.g., platelet derived growth factor), immunomodulatory (e.g., neutrophil-activating peptide 2), and adhesive (e.g., platelet endothelial cell adhesion molecule) proteins. (hindawi.com)
Shotgun tandem mass spectrometry-based peptide sequencing using programs such as SEQUEST allows high-throughput identification of peptides, which in turn allows identification of corresponding proteins. (washington.edu)
The differentially expressed proteins were analyzed by a MALDI-TOF-TOF mass spectrometer, and the identified proteins were investigated and categorized using bioinformatics. (wjgnet.com)
Identification is the process of determining the identity of the proteins, often done through mass spectrometry or protein sequencing. (proprofs.com)
It helps in identifying proteins by measuring the mass-to-charge ratio of ions produced from the protein sample. (proprofs.com)
In fact, when applied to a set of spectra from cataractous lenses proteins from a 93-year old patient, spectral networks were able to capitalize on the highly correlated peaks in spectra from variants of the same peptide to rediscover the modifications identified by database search methods and additionally discovered several novel modification events. (nih.gov)
Tal08 transcription complexes had been prepared from fungus YTT3675 cells using the Tal08 minichromosome 20 and Dynal beads (Invitrogen) cross-linked to anti-Flag M2 antibody (Sumanasekera (SGD_2010) or ST 2825 individual Uniprot (uni280910) focus on and decoy concatenated proteins data source 22 23 All decoy directories had been developed by reversing the sequences in the mark directories. (cancer-ecosystem.com)
However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)
Most commonly, this approach leverages high-resolution mass spectrometric measurements of proteolyzed proteins, combined with tandem peptide fragmentation to match observed spectra with those expected from their amino acid composition. (biorxiv.org)
11 And human diseases, including cancer in particular, tend to be defined by the presence of proteins with altered and pathogenic sequences. (biorxiv.org)
The approach combined proteins/peptides sequence information retrieved by specific enzymatic digestions (single and dual proteolytic enzymes) with protein digestibility information disclosed by means of in-vitro simulated human gastroduodenal digestion experiments. (uniba.it)
A database was constructed with the developed tool, and it was used to identify caspase target proteins from tandem mass spectrometry data from two different proteomic experiments. (biomedcentral.com)
We have developed Pripper, a tool for reading an arbitrary number of proteins in FASTA format, predicting their caspase cleavage sites and outputting the cleaved sequences to a new FASTA format sequence file. (biomedcentral.com)
The prediction of caspase cleavage sites from proteins is not a trivial task due to the heterogeneity of target sequences, and several different tools have been developed to predict caspase cleavage sites from individual proteins. (biomedcentral.com)
Consequently, a lot of effort is put into identifying the constituent proteins using mass spectrometric methods. (lu.se)
Cell proteins were analysed with 2-dimensional electrophoresis and differentially expressed proteins were identified by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. (who.int)

De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels et al. (wikipedia.org)
We introduce Spectralis, a new de novo peptide sequencing method for tandem mass spectrometry. (biorxiv.org)
Spectralis leverages several innovations including a new convolutional neural network layer connecting peaks in spectra spaced by amino acid masses, proposing fragment ion series classification as a pivotal task for de novo peptide sequencing, and a new peptide-spectrum confidence score. (biorxiv.org)
PepNovo serves as a high throughput de novo peptide sequencing tool for tandem mass spectrometry data. (ucsd.edu)
Second, I will present Spectralis, an algorithm for de novo peptide sequencing, i.e. reference-free identification of peptides from tandem mass spectrometry data [2]. (tum.de)

An interchain cross-link between two beta subunits was found in two tandem mass spectra. (nih.gov)
In contrast to steady-state protein abundance, which may be quantified directly in mass spectrometry (MS) by spectral intensity 16 , 17 or sampling frequency 18 , 19 , protein turnover rates cannot be predicted from steady-state data 20 , requiring instead methods that can distinguish old and new protein molecules in mass spectra 11 , 21 . (nature.com)
Recently, tandem mass spectrometry (MS/MS) based approaches seemed to be reaching the limit on the amount of information that could be extracted from MS/MS spectra. (nih.gov)
However, a closer look reveals that a common limiting procedure is to analyze each spectrum in isolation,even though high throughput mass spectrometry regularly generates spectra from related peptides. (nih.gov)
By capitalizing on this redundancy we show that, similarly to the alignment of protein sequences, unidentified MS/MS spectra can also be aligned for the identification of modified and unmodified variants of the same peptide. (nih.gov)
Spectral networks algorithms for de novo interpretation of tandem mass spectra / Nuno Bandeira. (nih.gov)
This new fragmentation scheme provides richer spectra and substantially increases the peptide sequence coverage and confidence in peptide identification. (analyteguru.com)
The type of mass spectrometer used to generate the experimental spectra. (ucsd.edu)
Additionally, we report TOF-TOF data obtained with monoisotopic precursor ion selection to provide clear product-ion mass spectra for each compound. (jeolusa.com)
Four types of product ions are identified for the high-energy CID product-ion mass spectra of sodiated PMMA ions. (jeolusa.com)
Additionally, we show that the TOF-TOF mode can be used to distinguish lysine and glutamine in these peptides by comparing the peak area ratio between a ions and d ions in the high-energy CID mass spectra. (jeolusa.com)
Current approaches for peptide and protein identification use advanced statistical and graphical methods to match mass spectra and estimate their confidence. (biorxiv.org)
With the exception of completely de novo mass spectrometry identification algorithms which currently lack the requisite accuracy and efficiency for genome-scale studies, all current methods depend on matching observed mass spectra to reference proteome databases. (biorxiv.org)
The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. (lu.se)
The goal is to assign acquired spectra to known peptide sequences and potential co- and post-translational modifica- tions. (lu.se)
These approaches depend on sequence databases that are used by the engines to match real spectra to theoretical in silico spectra. (lu.se)

and so on) that read raw spectral files , identify and quantify peptide ions. (bioconductor.org)
CID produces sequence-informative fragmentation and unambiguous determination of the conjugation site is possible on the basis of mass shifts of resultant fragment ions. (cdc.gov)
In these experiments, CID is performed in a multiplexed manner (e.g. alternating low and high collision energy scans) to allow high mass accuracy scans of parent and daughter fragment ions that may be temporally correlated in silico post run. (cdc.gov)
Peptide byproducts could be identified from the series of multiply charged ions observed, even when some of these peptides eluted from the HPLC with similar retention times. (elsevierpure.com)
The distinctive fragment ions from this cleavage were also observed for the peptides containing the Tmg and Dpg functionalities on the Dap side chain. (elsevierpure.com)
On the other hand, MALDI is generally considered unsuitable for low molecular weight compounds because the matrix ions interfere with sample ion detection in the low mass region. (jeolusa.com)
However, if these low m/z ions can be separated from each other and distinguished with sufficiently high mass resolving power, then MALDI can be expanded to the analysis of low-molecular-weight compounds. (jeolusa.com)
The 2nd TOF has (a) 20 kV high-energy CID, (b) monoisotopic precursor ion selection, and (c) no PSD ions in the product ion mass spectrum. (jeolusa.com)

The site(s) of diisocyanate conjugation upon the model protein(s) are characterized by enzymatic digestion of the conjugated protein, followed by fragmentation of the resultant enzymatic peptides by collision-induced dissociation (CID) in a quadrupole time-offlight (qTOF) mass spectrometer. (cdc.gov)
Lysine and glutamine are not easily distinguished by the most common approaches to peptide sequencing which involve mass spectrometers with low to moderate resolving power and low-energy collision-induced dissociation (CID). (jeolusa.com)

Characterization of diisocyanate haptenation of serum albumin by multiplexed tandem mass spectrometry. (cdc.gov)
2017. Characterization and Identification of Dityrosine Cross-Linked Peptides Using Tandem Mass Spectrometry. . (oregonstate.edu)
Mass Spectrometer at Arizona State University (ASU) Secondary Ion Mass Spectrometry (SIMS) SIMS is a technique for the characterization of solid surfaces and thin films. (esotech.org)
Given the global information provided by the designed proteomic approach, the in silico risk assessment not only tackled toxicity implication for celiac disease patients, but also scouted for immunogenic sequences relevant for wheat allergic patients, achieving a comprehensive characterization of the protein profile of the selected genotypes. (uniba.it)

Such an experiment allows greatly improved sequence coverage over more traditional "data-directed" experiments that require the instrument to make real-time decisions about which m/z ratios to select for fragmentation and often fail to target low abundance peptides that would otherwise be of interest to the analyst. (cdc.gov)
Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. (analyteguru.com)
Inducing 2-fold fragmentation by combining electron-transfer and higher-energy collision dissociation (EThcD) generates dual fragment ion series and facilitates extensive peptide backbone fragmentation. (analyteguru.com)
A unique fragmentation for the β,γ-bond of the Dap side chain was demonstrated and could be used to identify linear peptide byproducts. (elsevierpure.com)
2010-04-07 This putative identification is corroborated by mass spectrometric fragmentation, isotope labeling, and a gene silencing experiment. (firebaseapp.com)

Positive and negative peptides were more readily distinguished in training set data acquired on a QTOF compared to an ion trap mass spectrometer. (washington.edu)
A variety of mass spectrometer types, including magnetic sector, quadrupole, time-of-flight, and ion trap, have and will continue to deepen our understanding of the formation and evolution of exploration targets like the surfaces and atmospheres of planets and their moons. (frontiersin.org)
Peptides were analyzed in a mass spectrometer nanoESI qQTOF (5600 TripleTOF, ABSCIEX). (datadryad.org)
2018. Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer. . (oregonstate.edu)
We have demonstrated this by using the JEOL MALDI SpiralTOF mass spectrometer The innovative Spiral orbital technology consisting of 4 sets of toroidal electrical sector and Matsuda plates provides ultra-high mass resolving power combined with high ion transmission. (jeolusa.com)
In this study, we analyzed several oligosaccharides by using the JMS-S3000 SpiralTOF-TOF tandem mass spectrometer system. (jeolusa.com)
Gcn4 complex and its own MudPIT evaluation using an LCQ quadrupole ion snare mass spectrometer (Thermofisher) have already been previously referred to 19. (cancer-ecosystem.com)

This method required 10 microliters of serum and utilizes liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and isotope dilution for quantification. (cdc.gov)

We combined High-Resolution Mass Spectrometry and transcriptome analysis to study the OM composition of the axial skeleton and the sclerites. (biomedcentral.com)

The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data. (wikipedia.org)
The lectin showed affinity only for the glycoproteins fetuin, asialofetuin, mucin type III, and bovine submaxillary mucin type I. The complete amino acid sequences of two isoforms of ALL, named ALL-a and ALL-b, were determined by a combination of Edman degradation and overlapped peptides sequenced by tandem mass spectrometry. (bvsalud.org)
In both cases, the peptide pools were characterized by discovery analysis with liquid chromatography high-resolution tandem mass spectrometry, and specific amino acid sequences were identified via commercial software. (uniba.it)

The ether bond internal to N- acetylmuramic acid was cleaved with 3% ammonia, and the resulting lactoyl peptides were separated by reversed-phase, high-performance liquid chromatography for sequencing by tandem mass spectrometry (Qstar Pulsar I). (cdc.gov)
A BLAST search of internal peptide sequences obtained by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis suggested that the enzyme belonged to the GH27 family. (nih.gov)
Protein and peptide chromatography prior to MS analysis can partly address this issue. (hindawi.com)
In the first dimension, ion-exchange chromatography (IEC) separates peptides based on ionic interactions with the solid phase and an increasing salt buffer. (hindawi.com)
Liquid chromatography and tandem mass spectrometry (LC-MS/MS) were performed. (datadryad.org)
This protocol describes the peptidomic analysis of organoid lysates, FACS-purified cell populations, and 2D culture secretions by liquid chromatography mass spectrometry (LC-MS). Currently, most peptides are quantified by ELISA, limiting the peptides that can be studied. (cam.ac.uk)
Samples were then separated via liquid chromatography and detected via tandem mass spectrometry as previously reported (Pantazides et. (cdc.gov)

Modern flight-capable mass spectrometers, in combination with various sample processing, separation, and ionization techniques enable sensitive detection of chemical biosignatures. (frontiersin.org)
There are many applications of oligosaccharides in which various ionization techniques and mass spectrometers were used for their analysis [1]. (jeolusa.com)
The Desktop Spectrometry Starter Kit is only one part in an experimental setup, and the following shows where it fits in an overall diagram of a lab spectrometric setup: There are many, many different types of spectrometry and spectrometers -- many don't even measure light. (esotech.org)

The CSV document was parsed using the in-house Perl script process4peptide.pl to kind the validated PSMs into lists of full- half- or non-canonical tryptic peptide consensus sequences. (cancer-ecosystem.com)
Mass spectral analysis of the silver-stained band uncovered five tryptic peptides with masses that matched peptides from an Aedes aegypti lysozyme, which we had previously characterized from the Aag-2 mosquito cell line. (umn.edu)
The full length cDNA sequence was used to deduce the sequences and masses of theoretical tryptic peptides that would be detected after matrix-assisted laser desorption ionization time of flight (MALDI-TOF) and tandem mass spectrometry (MS/MS). In aggregate, this analysis uncovered seven peptides that encoded 75 of the 125 amino acids in the mature Ae. (umn.edu)

Here, we delve into the search for extraterrestrial chemical and morphological biosignatures and examine several possible approaches to agnostic life detection using mass spectrometry. (frontiersin.org)

The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. (biomedcentral.com)

Native mass spectrometry (native MS) is defined as the process whereby large biomolecules and complexes thereof can be transferred from a three-dimensional, functional existence in a condensed liquid phase to the gas phase via the process of electrospray ionization mass spectrometry … Spectrometry is based on interactions between matter and energy. (esotech.org)

The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. (lookformedical.com)

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)

Both modified and unmodified peptides have to be present in the sample to be detected. (lu.se)

On-line HPLC-ion spray mass spectrometry was more practical and useful than conventional HPLC alone for characterizing the products of these cyclization reactions. (elsevierpure.com)

Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. (wikipedia.org)
performs statistical analysis steps, that follow peptide identification and quantitation. (bioconductor.org)
In tandem with cutting-edge instrument platforms, research in data processing and data analysis on Earth-based (Terran) astrobiology analogs and on extraterrestrial materials also serves to increase the breadth of interpretations possible with mission data. (frontiersin.org)
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)
Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships. (lookformedical.com)
Mass [10] together with information on modifications induced by sample prepa- ration procedures for mass spectrometric analysis, but mass changes are only given as integer values. (lu.se)

Peptide identification algorithms fall into two broad classes: database search and de novo search. (wikipedia.org)

1990). Mass spectrometry data format: for a list of mass spectrometry data viewers and format converters. (wikipedia.org)
We studied the problem of detecting cross-linked peptides and cross-linked amino acids from tandem mass spectral data. (nih.gov)
2. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. (cdc.gov)
Here we report the use of Spiral technology to collect high mass-resolving power and high mass-accuracy data for eight triazine compounds. (jeolusa.com)
The novel algorithm runs on the three stage procedure: data washing data refining through a SVM-based decision function and your final data refining stage predicated on proteolytic peptide patterns. (cancer-ecosystem.com)
The most common data representation is the mass spectrum. (esotech.org)
Mass spectrometry produces various types of data. (esotech.org)
Comparison of Probability and Likelihood Models for Peptide Identification From Tandem Mass Spectrometry Data. (scitepress.org)
For the data sets used in this study, known mass differences are detected at electron mass ac- curacy or better. (lu.se)

To achieve high accuracy, a genome sequence database used for matching peptides was created and carefully curated. (chalmers.se)
We developed a method that can leverage large genome datasets to identify conserved elements without sequence alignment [1]. (tum.de)
PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
Washington University in St. Louis, Genome Sequencing Center. (scitepress.org)
Whole-genome sequencing of VR-MSSA, VS-MSSA, and 2 representatives of the Chilean/Cordobes clone (M1, M91) was performed by using MiSeq PacBio RS II (Illumina, San Diego, CA, USA) to close the VR-MSSA genome ( 5 ) (online Technical Appendix). (cdc.gov)

In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. (wikipedia.org)
The 47 protein sequences in Fasta format used in these experiments. (washington.edu)

The pMMO contains at least three subunits, of approximately 45, 27, and 23 kDa in molecular mass. (ncl.edu.tw)

We have applied a machine learning algorithm, called the support vector machine, to discriminate between correctly and incorrectly identified peptides using SEQUEST output. (washington.edu)
Each peptide was characterized by SEQUEST-calculated features such as delta Cn and Xcorr, measurements such as precursor ion current and mass, and additional calculated parameters such as the fraction of matched MS/MS peaks. (washington.edu)
Our outcomes demonstrate De-Noise boosts peptide identification in comparison to various other methods used to process the peptide sequence matches assigned by SEQUEST. (cancer-ecosystem.com)

However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)

The trained SVM classifier performed significantly better than previous cutoff-based methods at separating positive from negative peptides. (washington.edu)

abstract = "Protein chemistry and cDNA sequencing were used to identify an Aedes albopictus mosquito lysozyme secreted after treatment of cultured cells with heat-killed bacteria. (umn.edu)

The peptide list was screened for in silico toxicity/immunogenicity risk assessment, with the aid of various open-source bioinformatics tools for epitopes matching. (uniba.it)

The use of 13 features, including four new parameters, significantly improved the separation between positive and negative peptides. (washington.edu)

The proposed method is novel because it works independently of protein sequence databases and without any prior knowledge about modifica- tions. (lu.se)

Thus, the principle of protein or peptide haptenation could be used in in vitro assays to predict the sensitization potential of a new chemical entity. (cdc.gov)

In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). (lookformedical.com)

But despite valuable contributions, the road to a understanding of protein behavior is still hurdled by significant difficulties in the extensive identification of unexpected post-translational modifications and highly modified peptides. (nih.gov)
Increasing peptide sequence coverage by tandem mass spectrometry improves confidence in database search-based peptide identification and facilitates mapping of post-translational modifications and de novo sequencing. (analyteguru.com)

Peptides were then loaded onto an analytical column (LC Column, 3 µ C18-CL, 75 umx12cm, Nikkyo) equilibrated in 5% acetonitrile 0.1% FA (formic acid). (datadryad.org)
Mass spectrometry is an analytical tool useful for measuring the mass-to-charge ratio (m/z) of one or more molecules present in a sample. (esotech.org)

The authors recognize the Mass Spectrometry Consortium for the Life Sciences at the University of Minnesota and various supporting agencies, including the National Science Foundation for Major Research Instrumentation grant 9871237, used to purchase the instruments described in this study. (umn.edu)

In particular, tandem mass spectrometry techniques are often used to sequence these molecules. (jeolusa.com)
The Applications in human mineral Isotopic labeling of compounds is a non-radioactive method of labeling, provides site-specific investigation of structures, makes molecules easily detectable by mass spectrometry and NMR, maintaining the physico-chemical properties of the target molecule, and is cost-effective and easy to use. (firebaseapp.com)

Complete amino acid sequence consisted of 229 residues, including a FReD in the N-terminal. (bvsalud.org)
The chemical modification used to treat the cysteine residues in the peptide (typically a +57 Carbamidomethylation is used). (ucsd.edu)

We trained the model on over 800 fungal species and demonstrated its utility for sequence motif detection and for deriving state-of-the-art performance predictors for a range of gene regulatory prediction tasks. (tum.de)
We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein mod- ifications. (lu.se)

Cambridge Isotope Laboratories offers a complete listing of Stable Isotope Labeled Mass Spec for all your research needs. (firebaseapp.com)

Mass spectrometry is an example of a type of spectrometry, and it measures masses within a chemical sample through their mass-to-charge ratio. (esotech.org)
The Mass Distance Fin- gerprint is calculated from high accuracy measured peptide masses. (lu.se)
PTMs from this list in conjunction with a protein sequence and a few precursor masses. (lu.se)

All peaks +/- 17Da around precursor mass are deleted. (ucsd.edu)

Anatomy10

Organisms11

Diseases3

Chemicals and Drugs87

Analytical, Diagnostic and Therapeutic Techniques and Equipment71

Phenomena and Processes59

Disciplines and Occupations7

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Information Science9

Named Groups1

Health Care11

Geographicals1

Proteomics15

Proteins22

Novo peptide5

Spectra16

Ions8

Collision-induced diss2

Characterization4

Fragmentation5

Spectrometer7

Quantification1

High-resolution mass spectrometry1

Amino acid sequences3

Chromatography7

Spectrometers3

Tryptic3

Approaches1

Proteomic experiments1

Electrospray1

Enzymatic1

Specific amino acid1

Modified and unmodified1

HPLC1

Analysis7

Algorithms1

Data9

Genome5

Experiments2

Molecular1

SEQUEST3

Humans1

Methods1

Abstract1

Bioinformatics1

Separation1

Protein sequence databases1

Haptenation1

Fragments1

Post-translational2

Analytical2

Life Sciences1

Molecules2

Residues2

Detection2

Isotope1

Masses3

Peaks1