Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

Venable, John D.; Dong, Meng‐Qiu; Wohlschlegel, James A.; Dillin, Andrew; Yates, John R.

doi:10.1038/nmeth705

Cited by 706 publications

(658 citation statements)

References 18 publications

Supporting

Mentioning

651

Contrasting

Unclassified

Order By: Relevance

“…For example, average peptide ion abundance ratios determined from LTQ scans were 0.8, 2.31, and 4.76 for the 1:1, 5:1, and 10:1 standards respectively. Similar results have been published previously 4,23 . In contrast, peptide ion abundance ratios determined from Orbitrap MS scans were generally accurate within these same standard mixtures (i.e., average ratios were 1.07, 5.30, and 12.27 for the 1:1, 5:1, and 10:1 standards respectively).…”

Section: Evaluation Of Ltq-orbitrap Performance Using Yeast Standard supporting

confidence: 93%

Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer

et al. 2007

Self Cite

View full text Add to dashboard Cite

The quantitative analysis of complex biological samples has emerged as a key research area in the field of proteomics. Although quantitative proteomic experiments remain challenging, these strategies have been greatly facilitated by the development of newer high-performance mass spectrometers. In this work, we have evaluated the use of the LTQ-Orbitrap, a hybrid mass spectrometer in which a linear ion trap is coupled to an Orbitrap mass analyzer, for quantitative analyses. By analyzing a range of yeast protein standards, we found that the high mass accuracy, high resolution, large ion capacity, and large dynamic range of the LTQ-Orbitrap led to a significant improvement in the number and quality of the peptide ratio measurements compared to similar analyses done on the LTQ. We also successfully quantified protein expression differences that occur in metabolically labeled rat synapses during brain development to further demonstrate the suitability of the LTQ-Orbitrap for the comparative analysis of complex tissue samples.

show abstract

Section: Evaluation Of Ltq-orbitrap Performance Using Yeast Standard supporting

confidence: 93%

Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer

et al. 2007

Self Cite

View full text Add to dashboard Cite

show abstract

“…MudPIT Data Analysis-RAW files were extracted into ms2 file format (35) using RAW_Xtract version 1.0 (36). MS/MS spectra were searched using SEQUEST version 27 (revision 9) (37) with a peptide mass tolerance of 50 ppm and searched against a protein database combining non-redundant 5439 P. falciparum (PlasmoDB release 5.5) and 30,552 human proteins (NCBI 2008-03-04 release) as well as 162 usual contaminants, such as human keratins, IgGs, and proteolytic enzymes.…”

Section: Methodsmentioning

confidence: 99%

Unraveling the Ubiquitome of the Human Malaria Parasite

Ponts

Saraf

Chung

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Malaria is one of the deadliest infectious diseases worldwide. The most severe form is caused by the eukaryotic protozoan parasite Plasmodium falciparum. Recent studies have highlighted the importance of post-translational regulations for the parasite's progression throughout its life cycle, protein ubiquitylation being certainly one of the most abundant. The specificity of its components and the wide range of biological processes in which it is involved make the ubiquitylation pathway a promising source of suitable targets for anti-malarial drug development. Here, we combined immunofluorescent microscopy, biochemical assays, in silico prediction, and mass spectrometry analysis using the multidimensional protein identification technology, or MudPIT, to describe the P. falciparum ubiquitome. We found that ubiquitin conjugates are detected at every morphological stage of the parasite erythrocytic cycle. Furthermore, we detected that more than half of the parasite's proteome represents possible targets for ubiquitylation, especially proteins found to be present at the most replicative stage of the asexual cycle, the trophozoite stage. A large proportion of ubiquitin conjugates were also detected at the schizont stage, consistent with a cell activity slowdown to prepare for merozoite differentiation and invasion. Finally, for the first time in the human malaria parasite, our results strongly indicate the presence of heterologous mixed conjugations, SUMO/UB. This discovery suggests that sumoylated proteins may be regulated by ubiquitylation in P. falciparum. Altogether, our results present the first stepping stone toward a better understanding of ubiquitylation and its role(s) in the biology of the human malaria parasite.

show abstract

“…Digital Mapping of Immunopeptidomes in DIA Mode-DIA is an unbiased MS technique that combines the advantages of DDA and S/MRM (104). Since the introduction of its concept in 2004, several DIA strategies have been described and were reviewed in detail (66,(105)(106)(107).…”

Section: Identification and Quantification Of Mhc-associated Peptidesmentioning

confidence: 99%

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Caron

Kowalewski

Koh

et al. 2015

Molecular & Cellular Proteomics

197

118

View full text Add to dashboard Cite

The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field. Molecular & Cellular

show abstract

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

Cited by 706 publications

References 18 publications

Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer

Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer

Unraveling the Ubiquitome of the Human Malaria Parasite

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Contact Info

Product

Resources

About