Strategy for qualitative and quantitative analysis in proteomics based on signature peptides

Ji, Junyan A.; Chakraborty, Asish; Geng, Ming; Zhang, Xiang; Ahmad, A.L.; Bina, Minou; Regnier, Fred E.

doi:10.1016/s0378-4347(00)00192-4

Cited by 210 publications

(177 citation statements)

References 16 publications

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“…In such cases another approach must be taken, applying alternative (e.g. amine-reactive) chemistries and fractionation principles (43). Given the sensitivity of ion trap LC-MS/MS the detection limit and dynamic range of this technique are ultimately determined by sample complexity, because incompletely resolved peptides contribute to the background noise in CID spectra.…”

Section: Validation Of Quantitation From Ms/msmentioning

confidence: 99%

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Selective Detection of Membrane Proteins Without Antibodies

Arnott¹,

Kishiyama²,

Luis³

et al. 2002

Molecular & Cellular Proteomics

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A method has been developed, called the mass western experiment in analogy to the Western blot, to detect the presence of specific proteins in complex mixtures without the need for antibodies. Proteins are identified with high sensitivity and selectivity, and their abundances are compared between samples. Membrane protein extracts were labeled with custom isotope-coded affinity tag reagents and digested, and the labeled peptides were analyzed by liquid chromatography-tandem mass spectrometry. Ions corresponding to anticipated tryptic peptides from the proteins of interest were continuously subjected to collision-induced dissociation in an ion trap mass spectrometer; heavy and light isotope-coded affinity tag-labeled peptides were simultaneously trapped and fragmented accomplishing identification and quantitation in a single mass spectrum. This application of ion trap selective reaction monitoring maximizes sensitivity, enabling analysis of peptides that would otherwise go undetected. The cell surface proteins prostate stem cell antigen (PSCA) and ErbB2 were detected in prostate and breast tumor cell lines in which they are expressed in known abundances spanning orders of magnitude. Molecular & Cellular Proteomics 1:148 -156, 2002.

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Section: Validation Of Quantitation From Ms/msmentioning

confidence: 99%

“…Detection of such proteins will require additional fractionation of peptides, either by selection of different peptide subsets (e.g. histidine-containing sequences) (43) or tandem chromatographic separations (8,11,12).…”

Section: Validation Of Quantitation From Ms/msmentioning

confidence: 99%

Selective Detection of Membrane Proteins Without Antibodies

Arnott¹,

Kishiyama²,

Luis³

et al. 2002

Molecular & Cellular Proteomics

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show abstract

“…Rather simple labeling protocols make use of acetylation or acylation of amino groups for quantitative proteomics. For example, mass differences of 3 Da (e.g., by trideutero-acetylation [36] or 13 C-propionylation) or 4 Da (e.g., by succinylation [37]) can be introduced. Reductive dimethylation also yields a mass increase in 4 Da when deuterated formaldehyde is used [38].…”

Section: Isotope Labeling Of Amino Groups At the Peptide Levelmentioning

confidence: 99%

Stable isotopic labeling in proteomics

et al. 2008

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Labeling of proteins and peptides with stable heavy isotopes (deuterium, carbon-13, nitrogen-15, and oxygen-18) is widely used in quantitative proteomics. These are either incorporated metabolically in cells and small organisms, or postmetabolically in proteins and peptides by chemical or enzymatic reactions. Only upon measurement with mass spectrometers holding sufficient resolution, light, and heavy labeled peptide ions or reporter peptide fragment ions segregate and their intensity values are subsequently used for quantification. Targeted use of these labels or mass tags further leads to specific monitoring of diverse aspects of dynamic proteomes. In this review article, commonly used isotope labeling strategies are described, both for quantitative differential protein profiling and for targeted analysis of protein modifications.

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“…However, it could be very large due to unknown and/or ignored modifications of the experimental peptide. PepTiger provides a list of possible chemical and posttranslational modifications (PTMs) [31,32]. PepTiger supports two types of modification, fixed and variable.…”

Section: Scoring Schemementioning

confidence: 99%

PepTiger: Search Engine for Error-Tolerant Protein Identification from de Novo Sequences

Fedulova¹,

Ouyang²,

Buck³

et al. 2007

TOSPECJ

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Abstract:In recent years a number of de novo sequencing software products became available providing possible partial or complete amino acid sequence tags for MS/MS spectra of peptides. However, for a variety of reasons including spectral chemical noise and imperfect fragmentation these sequence tags almost always contain errors. Additional difficulties arise from actual protein sequence variation and post-translational modifications. We present a search engine named PepTiger which is capable of correctly matching de novo sequence tags with errors to protein sequences in a protein database. The algorithm is based on approximate string matching followed by a novel scoring procedure which takes into account mass differences and the string distance between de novo sequence and matched peptides and similarities between theoretical and experimental MS/MS spectra. Comparison of PepTiger with other protein identification software shows that PepTiger is better able to assign de novo sequence tags with errors to the correct peptide sequences.

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Strategy for qualitative and quantitative analysis in proteomics based on signature peptides

Cited by 210 publications

References 16 publications

Selective Detection of Membrane Proteins Without Antibodies

Selective Detection of Membrane Proteins Without Antibodies

Stable isotopic labeling in proteomics

PepTiger: Search Engine for Error-Tolerant Protein Identification from de Novo Sequences

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