Bioinformatics for LC-MS/MS-Based Proteomics (Q37788630)

23 August 2017

title

Bioinformatics for LC-MS/MS-based proteomics (English)

1 reference

23 August 2017

Bioinformatics for LC-MS/MS-Based Proteomics (English)

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

12 July 2024

1 reference

Richard J. Jacob

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20839098

12 July 2024

language of work or name

English

0 references

publication date

1 January 2010

1 reference

full work available at URL

23 August 2017

http://link.springer.com/content/pdf/10.1007/978-1-60761-780-8_4

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Methods in Molecular Biology

12 July 2024

published in

1 reference

23 August 2017

volume

658

1 reference

23 August 2017

page(s)

61-91

1 reference

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

23 August 2017

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Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides

12 July 2024

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Turbolytic: A peptide cleavage program for personal computers

12 July 2024

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MacProMass: a computer program to correlate mass spectral data to peptide and protein structures

12 July 2024

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Basic local alignment search tool

12 July 2024

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Simplification of high-energy collision spectra of peptides by amino-terminal derivatization.

12 July 2024

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Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database

12 July 2024

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Error-tolerant identification of peptides in sequence databases by peptide sequence tags

12 July 2024

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Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins

12 July 2024

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Interpreting peptide mass spectra by VEMS.

12 July 2024

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An alternative to tandem mass spectrometry: isoelectric point and accurate mass for the identification of peptides

12 July 2024

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In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

12 July 2024

16

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https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins.

12 July 2024

17

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https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

12 July 2024

18

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Probability-based protein identification by searching sequence databases using mass spectrometry data

12 July 2024

19

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https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Utility of Accurate Mass Tags for Proteome-Wide Protein Identification

12 July 2024

20

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Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

12 July 2024

21

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching.

12 July 2024

22

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data

12 July 2024

23

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https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

VIPER: an advanced software package to support high-throughput LC-MS peptide identification

12 July 2024

24

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins

12 July 2024

25

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A New Algorithm for the Evaluation of Shotgun Peptide Sequencing in Proteomics: Support Vector Machine Classification of Peptide MS/MS Spectra and SEQUEST Scores

12 July 2024

26

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

12 July 2024

27

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Accurate and sensitive peptide identification with Mascot Percolator

12 July 2024

28

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

12 July 2024

29

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies

12 July 2024

30

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Large-scale analysis of the yeast proteome by multidimensional protein identification technology

12 July 2024

31

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data

12 July 2024

32

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results

12 July 2024

33

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Efficient analysis and extraction of MS/MS result data from Mascot result files

12 July 2024

34

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Reporting protein identification data: the next generation of guidelines.

12 July 2024

35

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Guidelines for the next 10 years of proteomics

12 July 2024

36

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Mass spectrometry-based proteomics turns quantitative

12 July 2024

37

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

12 July 2024

38

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

12 July 2024

39

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry

12 July 2024

40

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant".

12 July 2024

41

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Proteolytic 18O-labeling strategies for quantitative proteomics

12 July 2024

42

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

12 July 2024

43

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

12 July 2024

44

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Automated comparative proteomics based on multiplex tandem mass spectrometry and stable isotope labeling

12 July 2024

45

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards

12 July 2024

46

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry

12 July 2024

47

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry.

12 July 2024

48

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Quantitative proteomic analysis by accurate mass retention time pairs

12 July 2024

49

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Quantitative proteomic analysis of drug-induced changes in mycobacteria

12 July 2024

50

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Quantification of gel-separated proteins and their phosphorylation sites by LC-MS using unlabeled internal standards: analysis of phosphoprotein dynamics in a B cell lymphoma cell line

12 July 2024

51

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

12 July 2024

52

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition

12 July 2024

53

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Error tolerant searching of uninterpreted tandem mass spectrometry data

12 July 2024

54

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Protein identification by spectral networks analysis

12 July 2024

55

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry

12 July 2024

56

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures.

12 July 2024

57

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

12 July 2024

58

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

POSTMan (POST-translational modification analysis), a software application for PTM discovery

12 July 2024

59

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Rapid and sensitive sequence comparison with FASTP and FASTA

12 July 2024

60

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Mobility labeling for parallel CID of ion mixtures.

12 July 2024

61

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A general precursor ion-like scanning mode on quadrupole-TOF instruments compatible with chromatographic separation.

12 July 2024

62

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: I. How much of the data is theoretically interpretable by s

12 July 2024

63

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

BIND--The Biomolecular Interaction Network Database

12 July 2024

65

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Gene ontology: tool for the unification of biology

12 July 2024

66

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

KEGG: Kyoto Encyclopedia of Genes and Genomes

12 July 2024

67

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The genome sequence of Schizosaccharomyces pombe

12 July 2024

68

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

LIMS and the art of MS proteomics

12 July 2024

70

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The proteomics standards initiative

12 July 2024

71

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories

12 July 2024

72

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The minimum information about a proteomics experiment (MIAPE)

12 July 2024

73

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

12 July 2024

The PeptideAtlas project

75

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

PRIDE: the proteomics identifications database

12 July 2024

76

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A uniform proteomics MS/MS analysis platform utilizing open XML file formats

12 July 2024

77

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data

12 July 2024

79

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Open mass spectrometry search algorithm

12 July 2024

80

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides

12 July 2024

81

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

TANDEM: matching proteins with tandem mass spectra

12 July 2024

82

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra

12 July 2024

83

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

12 July 2024

84

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model

12 July 2024

85

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

12 July 2024

86

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Multiple parameter cross-species protein identification using MultiIdent--a world-wide web accessible tool.

12 July 2024

87

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A strategy for rapid, high-confidence protein identification

12 July 2024

89

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A platform for accurate mass and time analyses of mass spectrometry data

12 July 2024

90

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Development and validation of a spectral library searching method for peptide identification from MS/MS.

12 July 2024

91

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Using BiblioSpec for creating and searching tandem MS peptide libraries

12 July 2024

92

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Clustering millions of tandem mass spectra

12 July 2024

93

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

MSight: an image analysis software for liquid chromatography-mass spectrometry

12 July 2024

94

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry

12 July 2024

95

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data

12 July 2024

96

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

12 July 2024

97

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

12 July 2024

98

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

mzAPI: a new strategy for efficiently sharing mass spectrometry data

12 July 2024

99

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Journal of Biomolecular Techniques

12 July 2024

100

18

7

D. J. Slotta

2007

1 reference

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MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

12 July 2024

101

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data

12 July 2024

102

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Proteomic characterization of the human centrosome by protein correlation profiling

12 July 2024

103

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

12 July 2024

104

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

12 July 2024

105

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

i-Tracker: for quantitative proteomics using iTRAQ.

12 July 2024

106

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human [...]

12 July 2024

107

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

DAnTE: a statistical tool for quantitative analysis of -omics data.

12 July 2024

108

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

A method for automatically interpreting mass spectra of 18O-labeled isotopic clusters.

12 July 2024

109

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry

12 July 2024

110

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Database independent detection of isotopically labeled MS/MS spectrum peptide pairs

12 July 2024

111

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Efficiency of database search for identification of mutated and modified proteins via mass spectrometry

12 July 2024

112

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data

12 July 2024

113

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data

12 July 2024

114

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry

12 July 2024

115

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

NovoHMM: a hidden Markov model for de novo peptide sequencing

12 July 2024

117

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

AUDENS: a tool for automated peptide de novo sequencing.

12 July 2024

118

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics

12 July 2024

119

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

PepNovo: de novo peptide sequencing via probabilistic network modeling

12 July 2024

121

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Evaluation of the efficiency of in-gel digestion of proteins by peptide isotopic labeling and MALDI mass spectrometry

12 July 2024

122

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

12 July 2024

123

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer

12 July 2024

124

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry

12 July 2024

125

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

12 July 2024

126

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

12 July 2024

127

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

MPSS: an integrated database system for surveying a set of proteins

12 July 2024

128

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data

12 July 2024

129

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The GOA database in 2009--an integrated Gene Ontology Annotation resource

12 July 2024

130

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

The need for a public proteomics repository

12 July 2024

131

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https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

Human Proteinpedia enables sharing of human protein data

12 July 2024

132

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https://api.crossref.org/works/10.1007/978-1-60761-780-8_4

12 July 2024

Identifiers

1 reference

23 August 2017

1 reference