Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics * □S (2008)
Wilhelm Haas, Brendan K. Faherty, Scott A. Gerber, Joshua E. Elias, Sean A. Beausoleil, Corey E. Bakalarski, ...
Mass spectrometers that provide high mass accuracy such as FT-ICR instruments are increasingly used in proteomic studies. Although the importance of accurately determined molecular masses for the...
Proteomic Profiling of γ-Secretase Substrates and Mapping of Substrate Requirements (2008)
Matthew L. Hemming, Joshua E. Elias, Steven P. Gygi, Dennis J. Selkoe
The presenilin/γ-secretase complex, an unusual intramembrane aspartyl protease, plays an essential role in cellular signaling and membrane protein turnover. Its ability to liberate numerous...
Tan, Jeanne M.M., Wong, Esther S.P., Kirkpatrick, Donald S., Pletnikova, Olga, Ko, Han Seok, Tay, Shiam-Peng, ...
Although ubiquitin-enriched protein inclusions represent an almost invariant feature of neurodegenerative diseases, the mechanism underlying their biogenesis remains unclear. In particular, whether...
Helmlinger, Dominique, Marguerat, Samuel, Villén, Judit, Gygi, Steven P., Bähler, Jürg, Winston, Fred
The SAGA complex is a conserved multifunctional coactivator known to play broad roles in eukaryotic transcription. To gain new insights into its functions, we performed biochemical and genetic...
Orion D. Weiner, Maike C. Rentel, Alex Ott, Glenn E. Brown, Mark Jedrychowski, Michael B. Yaffe, ...
The authors describe a group of multiprotein complexes, scaffolded by Hem-1 (a subset of which also contain WAVE2), that are involved in generating and maintaining cellular polarity in neutrophils.
Orion D. Weiner, Maike C. Rentel, Alex Ott, Glenn E. Brown, Mark Jedrychowski, Michael B. Yaffe, ...
Migrating cells need to make different actin assemblies at the cell's leading and trailing edges and to maintain physical separation of signals for these assemblies. This asymmetric control of...
Huang, Julie, Brito, Ilana L., Villén, Judit, Gygi, Steven P., Amon, Angelika, Moazed, Danesh
Silencing within the yeast ribosomal DNA (rDNA) repeats protects the integrity of this highly repetitive array by inhibiting hyperrecombination and repressing transcription from foreign promoters....
Xu, Jin, Zhong, Nan, Wang, Haoyong, Elias, Joshua E., Kim, Christina Y., Woldman, Irina, ...
Mutations in the DJ-1 gene cause early-onset autosomal recessive Parkinson's disease (PD), although the role of DJ-1 in the degeneration of dopaminergic neurons is unresolved. Here we show that the...
Xu, Jin, Zhong, Nan, Wang, Haoyong, Elias, Joshua E., Kim, Christina Y., Woldman, Irina, ...
Mutations in the DJ-1 gene cause early-onset autosomal recessive Parkinson's disease (PD), although the role of DJ-1 in the degeneration of dopaminergic neurons is unresolved. Here we show that the...
SILVER Helps Assign Peptides to Tandem Mass Spectra Using Intensity-Based Scoring (2004)
Francis D. Gibbons, Joshua E. Elias, Steven P. Gygi, Frederick P. Roth
redicted for peptides in a genome-derived database. Software using the latter approach has been more commonly adopted, with SEQUEST [2] and Mascot [3] being popular examples. However, exhaustive...
Hierarchical phosphorylation of the translation inhibitor 4E-BP1 (2001)
Gingras, Anne-Claude, Raught, Brian, Gygi, Steven P., Niedzwiecka, Anna, Miron, Mathieu, Burley, Stephen K., ...
Regulation of 4E-BP1 phosphorylation: a novel two-step mechanism (1999)
Gingras, Anne-Claude, Gygi, Steven P., Raught, Brian, Polakiewicz, Roberto D., Abraham, Robert T., Hoekstra, Merl F., ...
Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
Gygi, Steven P., Corthals, Garry L., Zhang, Yanni, Rochon, Yvan, Aebersold, Ruedi
Proteome analysis is most commonly accomplished by a combination of two-dimensional gel electrophoresis (2DE) to separate and visualize proteins and mass spectrometry (MS) for protein identification....
Correlation between Protein and mRNA Abundance in Yeast
Gygi, Steven P., Rochon, Yvan, Franza, B. Robert, Aebersold, Ruedi
We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeast Saccharomyces cerevisiae growing at mid-log phase. The proteins contained in...
Panigrahi, Aswini K., Gygi, Steven P., Ernst, Nancy L., Igo, Robert P., Palazzo, Setareh S., Schnaufer, Achim, ...
RNA editing in kinetoplastid mitochondria inserts and deletes uridylates at multiple sites in pre-mRNAs as directed by guide RNAs. This occurs by a series of steps that are catalyzed by...
Four Related Proteins of the Trypanosoma brucei RNA Editing Complex
Panigrahi, Aswini K., Schnaufer, Achim, Carmean, Nicole, Igo, Robert P., Gygi, Steven P., Ernst, Nancy L., ...
RNA editing in kinetoplastid mitochondria occurs by a series of enzymatic steps that is catalyzed by a macromolecular complex. Four novel proteins and their corresponding genes were identified by...
Hoppe, Georg J., Tanny, Jason C., Rudner, Adam D., Gerber, Scott A., Danaie, Sherwin, Gygi, Steven P., ...
Transcriptional silencing at the budding yeast silent mating type (HM) loci and telomeric DNA regions requires Sir2, a conserved NAD-dependent histone deacetylase, Sir3, Sir4, histones H3 and H4, and...
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
Gerber, Scott A., Rush, John, Stemman, Olaf, Kirschner, Marc W., Gygi, Steven P.
A need exists for technologies that permit the direct quantification of differences in protein and posttranslationally modified protein expression levels. Here we present a strategy for the absolute...
Hitchcock, Amy L., Auld, Kathryn, Gygi, Steven P., Silver, Pamela A.
Ubiquitination of membrane-associated proteins can direct their proteasome-mediated degradation or activation at the endoplasmic reticulum (ER), as well as their endocytosis and intracellular...
Raught, Brian, Gingras, Anne-Claude, Gygi, Steven P., Imataka, Hiroaki, Morino, Shigenobu, Gradi, Alessandra, ...
The eukaryotic translation initiation factor 4G (eIF4G) proteins play a critical role in the recruitment of the translational machinery to mRNA. The eIF4Gs are phosphoproteins. However, the location...
Regulation of 4E-BP1 phosphorylation: a novel two-step mechanism
Gingras, Anne-Claude, Gygi, Steven P., Raught, Brian, Polakiewicz, Roberto D., Abraham, Robert T., Hoekstra, Merl F., ...
The multisubunit eukaryotic translation initiation factor (eIF) 4F recruits 40S ribosomal subunits to the 5′ end of mRNA. The eIF4F subunit eIF4E interacts directly with the mRNA 5′ cap...
Purification and architecture of the ubiquitous Wave complex
Gautreau, Alexis, Ho, Hsin-yi H., Li, Jiaxu, Steen, Hanno, Gygi, Steven P., Kirschner, Marc W.
The Wave proteins are major activators of the Arp2/3 complex. The ubiquitous Wave-2 is required for actin polymerization at the leading edge of migrating cells. Here we purify Wave-2 from HeLa cells....
Budding Yeast Silencing Complexes and Regulation of Sir2 Activity by Protein-Protein Interactions
Tanny, Jason C., Kirkpatrick, Donald S., Gerber, Scott A., Gygi, Steven P., Moazed, Danesh
Gene silencing in the budding yeast Saccharomyces cerevisiae requires the enzymatic activity of the Sir2 protein, a highly conserved NAD-dependent deacetylase. In order to study the activity of...
Large-scale characterization of HeLa cell nuclear phosphoproteins
Beausoleil, Sean A., Jedrychowski, Mark, Schwartz, Daniel, Elias, Joshua E., Villén, Judit, Li, Jiaxu, ...
Determining the site of a regulatory phosphorylation event is often essential for elucidating specific kinase–substrate relationships, providing a handle for understanding essential signaling...
BRCA1-Dependent Ubiquitination of γ-Tubulin Regulates Centrosome Number
Starita, Lea M., Machida, Yuka, Sankaran, Satish, Elias, Joshua E., Griffin, Karen, Schlegel, Brian P., ...
Proper centrosome duplication and spindle formation are crucial for prevention of chromosomal instability, and BRCA1 plays a role in this process. In this study, transient inhibition of BRCA1...
Roux, Philippe P., Ballif, Bryan A., Anjum, Rana, Gygi, Steven P., Blenis, John
Tuberous sclerosis complex (TSC) is a genetic disorder caused by mutations in either of the two tumor suppressor genes TSC1 or TSC2, which encode hamartin and tuberin, respectively. Tuberin and...
Ballif, Bryan A., Roux, Philippe P., Gerber, Scott A., MacKeigan, Jeffrey P., Blenis, John, Gygi, Steven P.
Reversible protein phosphorylation is an essential cellular regulatory mechanism. Many proteins integrate and are modulated by multiple phosphorylation events derived from complex signaling cues....
Weighing in on Ubiquitin: The Expanding Role of Mass Spectrometry-based Proteomics
Kirkpatrick, Donald S., Denison, Carilee, Gygi, Steven P.
Mass spectrometry-based proteomics has become an essential tool for qualitative and quantitative analysis of cellular systems. The biochemical complexity and functional diversity of the ubiquitin...
Weiner, Orion D, Rentel, Maike C, Ott, Alex, Brown, Glenn E, Jedrychowski, Mark, Yaffe, Michael B, ...
Migrating cells need to make different actin assemblies at the cell's leading and trailing edges and to maintain physical separation of signals for these assemblies. This asymmetric control of...
Hierarchical phosphorylation of the translation inhibitor 4E-BP1
Gingras, Anne-Claude, Raught, Brian, Gygi, Steven P., Niedzwiecka, Anna, Miron, Mathieu, Burley, Stephen K., ...
In most instances, translation is regulated at the initiation phase, when a ribosome is recruited to the 5′ end of an mRNA. The eIF4E-binding proteins (4E-BPs) interdict translation initiation by...
Liu, Libin, Jedrychowski, Mark P., Gygi, Steven P., Pilch, Paul F.
Fodrin or nonerythroid spectrin is an abundant component of the cortical cytoskeletal network in rat adipocytes. Fodrin has a highly punctate distribution in resting cells, and insulin causes a...
Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
Gygi, Steven P., Corthals, Garry L., Zhang, Yanni, Rochon, Yvan, Aebersold, Ruedi
Proteome analysis is most commonly accomplished by a combination of two-dimensional gel electrophoresis (2DE) to separate and visualize proteins and mass spectrometry (MS) for protein identification....
Correlation between Protein and mRNA Abundance in Yeast
Gygi, Steven P., Rochon, Yvan, Franza, B. Robert, Aebersold, Ruedi
We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeast Saccharomyces cerevisiae growing at mid-log phase. The proteins contained in...
Panigrahi, Aswini K., Gygi, Steven P., Ernst, Nancy L., Igo, Robert P., Palazzo, Setareh S., Schnaufer, Achim, ...
RNA editing in kinetoplastid mitochondria inserts and deletes uridylates at multiple sites in pre-mRNAs as directed by guide RNAs. This occurs by a series of steps that are catalyzed by...
Four Related Proteins of the Trypanosoma brucei RNA Editing Complex
Panigrahi, Aswini K., Schnaufer, Achim, Carmean, Nicole, Igo, Robert P., Gygi, Steven P., Ernst, Nancy L., ...
RNA editing in kinetoplastid mitochondria occurs by a series of enzymatic steps that is catalyzed by a macromolecular complex. Four novel proteins and their corresponding genes were identified by...
Hoppe, Georg J., Tanny, Jason C., Rudner, Adam D., Gerber, Scott A., Danaie, Sherwin, Gygi, Steven P., ...
Transcriptional silencing at the budding yeast silent mating type (HM) loci and telomeric DNA regions requires Sir2, a conserved NAD-dependent histone deacetylase, Sir3, Sir4, histones H3 and H4, and...
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
Gerber, Scott A., Rush, John, Stemman, Olaf, Kirschner, Marc W., Gygi, Steven P.
A need exists for technologies that permit the direct quantification of differences in protein and posttranslationally modified protein expression levels. Here we present a strategy for the absolute...
Hitchcock, Amy L., Auld, Kathryn, Gygi, Steven P., Silver, Pamela A.
Ubiquitination of membrane-associated proteins can direct their proteasome-mediated degradation or activation at the endoplasmic reticulum (ER), as well as their endocytosis and intracellular...
Raught, Brian, Gingras, Anne-Claude, Gygi, Steven P., Imataka, Hiroaki, Morino, Shigenobu, Gradi, Alessandra, ...
The eukaryotic translation initiation factor 4G (eIF4G) proteins play a critical role in the recruitment of the translational machinery to mRNA. The eIF4Gs are phosphoproteins. However, the location...
Hierarchical phosphorylation of the translation inhibitor 4E-BP1
Gingras, Anne-Claude, Raught, Brian, Gygi, Steven P., Niedzwiecka, Anna, Miron, Mathieu, Burley, Stephen K., ...
In most instances, translation is regulated at the initiation phase, when a ribosome is recruited to the 5′ end of an mRNA. The eIF4E-binding proteins (4E-BPs) interdict translation initiation by...
Regulation of 4E-BP1 phosphorylation: a novel two-step mechanism
Gingras, Anne-Claude, Gygi, Steven P., Raught, Brian, Polakiewicz, Roberto D., Abraham, Robert T., Hoekstra, Merl F., ...
The multisubunit eukaryotic translation initiation factor (eIF) 4F recruits 40S ribosomal subunits to the 5′ end of mRNA. The eIF4F subunit eIF4E interacts directly with the mRNA 5′ cap...
Purification and architecture of the ubiquitous Wave complex
Gautreau, Alexis, Ho, Hsin-yi H., Li, Jiaxu, Steen, Hanno, Gygi, Steven P., Kirschner, Marc W.
The Wave proteins are major activators of the Arp2/3 complex. The ubiquitous Wave-2 is required for actin polymerization at the leading edge of migrating cells. Here we purify Wave-2 from HeLa cells....
Budding Yeast Silencing Complexes and Regulation of Sir2 Activity by Protein-Protein Interactions
Tanny, Jason C., Kirkpatrick, Donald S., Gerber, Scott A., Gygi, Steven P., Moazed, Danesh
Gene silencing in the budding yeast Saccharomyces cerevisiae requires the enzymatic activity of the Sir2 protein, a highly conserved NAD-dependent deacetylase. In order to study the activity of...
Large-scale characterization of HeLa cell nuclear phosphoproteins
Beausoleil, Sean A., Jedrychowski, Mark, Schwartz, Daniel, Elias, Joshua E., Villén, Judit, Li, Jiaxu, ...
Determining the site of a regulatory phosphorylation event is often essential for elucidating specific kinase–substrate relationships, providing a handle for understanding essential signaling...
BRCA1-Dependent Ubiquitination of γ-Tubulin Regulates Centrosome Number
Starita, Lea M., Machida, Yuka, Sankaran, Satish, Elias, Joshua E., Griffin, Karen, Schlegel, Brian P., ...
Proper centrosome duplication and spindle formation are crucial for prevention of chromosomal instability, and BRCA1 plays a role in this process. In this study, transient inhibition of BRCA1...
Roux, Philippe P., Ballif, Bryan A., Anjum, Rana, Gygi, Steven P., Blenis, John
Tuberous sclerosis complex (TSC) is a genetic disorder caused by mutations in either of the two tumor suppressor genes TSC1 or TSC2, which encode hamartin and tuberin, respectively. Tuberin and...
Ballif, Bryan A., Roux, Philippe P., Gerber, Scott A., MacKeigan, Jeffrey P., Blenis, John, Gygi, Steven P.
Reversible protein phosphorylation is an essential cellular regulatory mechanism. Many proteins integrate and are modulated by multiple phosphorylation events derived from complex signaling cues....
Weiner, Orion D, Rentel, Maike C, Ott, Alex, Brown, Glenn E, Jedrychowski, Mark, Yaffe, Michael B, ...
Migrating cells need to make different actin assemblies at the cell's leading and trailing edges and to maintain physical separation of signals for these assemblies. This asymmetric control of...
Liu, Libin, Jedrychowski, Mark P., Gygi, Steven P., Pilch, Paul F.
Fodrin or nonerythroid spectrin is an abundant component of the cortical cytoskeletal network in rat adipocytes. Fodrin has a highly punctate distribution in resting cells, and insulin causes a...
Huang, Julie, Brito, Ilana L., Villén, Judit, Gygi, Steven P., Amon, Angelika, Moazed, Danesh
Silencing within the yeast ribosomal DNA (rDNA) repeats protects the integrity of this highly repetitive array by inhibiting hyperrecombination and repressing transcription from foreign promoters....
Johri, Atul K., Margarit, Immaculada, Broenstrup, Mark, Brettoni, Cecilia, Hua, Lei, Gygi, Steven P., ...
Group B Streptococcus (GBS) is an opportunistic organism that can harmlessly colonize the human gut, vagina, and rectum but can also cause pneumonia, sepsis, and meningitis in neonates born to...
Large-scale phosphorylation analysis of mouse liver
Villén, Judit, Beausoleil, Sean A., Gerber, Scott A., Gygi, Steven P.
Protein phosphorylation is a complex network of signaling and regulatory events that affects virtually every cellular process. Our understanding of the nature of this network as a whole remains...
The tumor suppressor CYLD regulates entry into mitosis
Stegmeier, Frank, Sowa, Mathew E., Nalepa, Grzegorz, Gygi, Steven P., Harper, J. Wade, Elledge, Stephen J.
Mutations in the cylindromatosis (CYLD) gene cause benign tumors of skin appendages, referred to as cylindromas. The CYLD gene encodes a deubiquitinating enzyme that removes Lys-63-linked ubiquitin...
Niu, Hengyao, Li, Xue, Job, Emily, Park, Caroline, Moazed, Danesh, Gygi, Steven P., ...
Mek1 is a meiosis-specific kinase in budding yeast which promotes recombination between homologous chromosomes by suppressing double-strand break (DSB) repair between sister chromatids. Previous work...
The ubiquitin–proteasome system regulates membrane fusion of yeast vacuoles
Kleijnen, Maurits F, Kirkpatrick, Donald S, Gygi, Steven P
Ubiquitination is known to regulate early stages of intracellular vesicular transport, without proteasomal involvement. We now show that, in yeast, ubiquitination regulates a late-stage, membrane...
The Septins Function in G1 Pathways that Influence the Pattern of Cell Growth in Budding Yeast
Egelhofer, Thea A., Villén, Judit, McCusker, Derek, Gygi, Steven P., Kellogg, Douglas R.
The septins are a conserved family of proteins that have been proposed to carry out diverse functions. In budding yeast, the septins become localized to the site of bud emergence in G1 but have not...
Profiling of UV-induced ATM/ATR signaling pathways
Stokes, Matthew P., Rush, John, MacNeill, Joan, Ren, Jian Min, Sprott, Kam, Nardone, Julie, ...
To ensure survival in the face of genomic insult, cells have evolved complex mechanisms to respond to DNA damage, termed the DNA damage checkpoint. The serine/threonine kinases ataxia...
Signaling networks assembled by oncogenic EGFR and c-Met
Guo, Ailan, Villén, Judit, Kornhauser, Jon, Lee, Kimberly A., Stokes, Matthew P., Rikova, Klarisa, ...
A major question regarding the sensitivity of solid tumors to targeted kinase inhibitors is why some tumors respond and others do not. The observation that many tumors express EGF receptor (EGFR),...
Unphosphorylated SR-Like Protein Npl3 Stimulates RNA Polymerase II Elongation
Dermody, Jessica L., Dreyfuss, Jonathan M., Villén, Judit, Ogundipe, Babatunde, Gygi, Steven P., Park, Peter J., ...
The production of a functional mRNA is regulated at every step of transcription. An area not well-understood is the transition of RNA polymerase II from elongation to termination. The S. cerevisiae...
Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis
Morita, Eiji, Sandrin, Virginie, Chung, Hyo-Young, Morham, Scott G, Gygi, Steven P, Rodesch, Christopher K, ...
TSG101 and ALIX both function in HIV budding and in vesicle formation at the multivesicular body (MVB), where they interact with other Endosomal Sorting Complex Required for Transport (ESCRT) pathway...
Proteomic Profiling of γ-Secretase Substrates and Mapping of Substrate Requirements
Hemming, Matthew L, Elias, Joshua E, Gygi, Steven P, Selkoe, Dennis J
The presenilin/γ-secretase complex, an unusual intramembrane aspartyl protease, plays an essential role in cellular signaling and membrane protein turnover. Its ability to liberate numerous...
Xu, Lai, Sowa, Mathew E., Chen, Jing, Li, Xue, Gygi, Steven P., Harper, J. Wade
Fused Toes (FTS) is a member of a small group of inactive variant E2 ubiquitin-conjugating enzyme domain-containing proteins of unknown function. Through proteomic analysis of FTS complexes purified...
A quantitative atlas of mitotic phosphorylation
Dephoure, Noah, Zhou, Chunshui, Villén, Judit, Beausoleil, Sean A., Bakalarski, Corey E., Elledge, Stephen J., ...
The eukaryotic cell division cycle is characterized by a sequence of orderly and highly regulated events resulting in the duplication and separation of all cellular material into two newly formed...
Wainszelbaum, Marisa J., Charron, Audra J., Kong, Chen, Kirkpatrick, Donald S., Srikanth, Priya, Barbieri, M. Alejandro, ...
Hominoid- and human-specific genes may have evolved to modulate signaling pathways of a higher order of complexity. TBC1D3 is a hominoid-specific oncogene encoded by a cluster of eight paralogs on...
Sir3-Nucleosome Interactions in Spreading of Silent Chromatin in Saccharomyces cerevisiae▿
Buchberger, Johannes R., Onishi, Megumi, Li, Geng, Seebacher, Jan, Rudner, Adam D., Gygi, Steven P., ...
Silent chromatin in Saccharomyces cerevisiae is established in a stepwise process involving the SIR complex, comprised of the histone deacetylase Sir2 and the structural components Sir3 and Sir4. The...
Helmlinger, Dominique, Marguerat, Samuel, Villén, Judit, Gygi, Steven P., Bähler, Jürg, Winston, Fred
The SAGA complex is a conserved multifunctional coactivator known to play broad roles in eukaryotic transcription. To gain new insights into its functions, we performed biochemical and genetic...
A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export
Hurt, Jessica A., Obar, Robert A., Zhai, Bo, Farny, Natalie G., Gygi, Steven P., Silver, Pamela A.
Coupling of messenger RNA (mRNA) nuclear export with prior processing steps aids in the fidelity and efficiency of mRNA transport to the cytoplasm. In this study, we show that the processes of export...