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Proteomics Resource Center

Rockefeller University

Contact Info:

Henrik Molina

1230 York Avenue

Box 105

New York, NY 10065

https://www.rockefeller.edu/proteomics/

Grants and Identifiers:

RRID: RRID:SCR_017797

Instrumentation:

Agilent 5977B GC/MSD

GC/MSD is used for environmental, chemical, petrochemical, food, forensic, pharmaceutical, and material testing. [Product Link]

RRID:SCR_019420

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Thermo LTQ Orbitrap XL ETD Hybrid Ion Trap-Orbitrap Mass Spectrometer

Thermo Scientific LTQ Orbitrap XL ETD Hybrid Ion Trap-Orbitrap Mass Spectrometer can be used to identify, characterize and quantify proteins and peptides using. This instrument is a comprehensive solution for a range of proteomics applications including complex PTM analysis; intelligent sequencing of peptides; top-down and middle-down analysis; label-free quantitation; or quantitation using stable isotope labeling methods such as TMT and iTRAQ. [Product Link]

RRID:SCR_020549

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Thermo LTQ XL Linear Ion Trap Mass Spectrometer

Ion trap mass spectrometer with Agilent 1100 HPLC system is used for a variety of studies including metabolite identification, stability testing, degradation products, and high-abundance quantitation. [Product Link]

RRID:SCR_020554

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Thermo Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer

Identify and quantify more proteins, peptides, lipids, glycans and small molecules accurately and in less time with the Thermo Scientific Q Exactive HF hybrid quadrupole-Orbitrap mass spectrometer. The Q Exactive HF system combines a state-of-the-art segmented quadrupole for high-performance precursor ion selection with a high-resolution, accurate-mass (HR/AM) ultra-high-field Orbitrap mass analyzer to deliver a superior combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity. Identify, quantify and confirm in a single analysis with a single instrument with the Q Exactive HF mass spectrometer. [Product Link]

RRID:SCR_020558

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Thermo Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer

Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer has increased performance and new options that enhance applications from confident DMPK qual/quan screening studies to characterization of intact monoclonal antibodies. [Product Link]

RRID:SCR_020556

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Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer

Spectrometer performs analysis including low level PTM analysis, multiplexed relative quantitation using isobaric tags, intact protein characterization, and MSn analysis of small molecules. System incorporates the brightest ion source, segmented quadrupole mass filter with improved selectivity and ion transmission, Advanced Vacuum Technology, and ETD HD. [Product Link]

RRID:SCR_020562

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Services Provided:

Mass Spectrometry

Metabolomics

Metabolomics Platform

Peptide Synthesis

Proteomics

Relevant Publications:

1.) Zhao H, Li J, Xiang Y, Malik S, Vartak SV, Veronezi GMB, Young N, Riney M, Kalchschmidt J, Conte A, Jung SK, Ramachandran S, Roeder RG, Shi Y, Casellas R, Asturias FJ (2024 Jul 25). An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Molecular cell, 84(14), 2648-2664.e10. . PMID: 38955181.


2.) Clark JF, Soriano P (2024 Jun 25). Diverse Fgfr1 signaling pathways and endocytic trafficking regulate mesoderm development. Genes & development, 38(9), 393-414. . PMID: 38834239.


3.) Hossain AA, Pigli YZ, Baca CF, Heissel S, Thomas A, Libis VK, Burian J, Chappie JS, Brady SF, Rice PA, Marraffini LA (2024 Apr 17). DNA glycosylases provide antiviral defence in prokaryotes Nature, 629(8011), 410-416. . PMCID: 11078745.


4.) Notti RQ, Yi F, Heissel S, Bush MW, Molina H, Molvi Z, Klebanoff CA, Walz T (2024 Apr 8). The resting state of the human T-cell receptor-CD3 complex. bioRxiv : the preprint server for biology, (), . . PMID: 37662363.


5.) Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A (2024 Mar 2). RTF2 controls replication repriming and ribonucleotide excision at the replisome Nature Communications, 15(), 1943. . PMCID: 10908796.


6.) Clark JF, Soriano P (2024 Feb 16). Diverse Fgfr1 signaling pathways and endocytic trafficking regulate early mesoderm development bioRxiv, (), 2024.02.16.580629. . PMCID: 10888970.


7.) Liu Y, Liu S, Tomar A, Yen FS, Unlu G, Ropek N, Weber RA, Wang Y, Khan A, Gad M, Peng J, Terzi E, Alwaseem H, Pagano AE, Heissel S, Molina H, Allwein B, Kenny TC, Possemato RL, Zhao L, Hite RK, Vinogradova EV, Mansy SS, Birsoy K (2023 Nov 17). Autoregulatory control of mitochondrial glutathione homeostasis. Science (New York, N.Y.), 382(6672), 820-828. doi: 10.1126/science.adf4154. PMID: 37917749.


8.) Kenny TC, Khan A, Son Y, Yue L, Heissel S, Sharma A, Pasolli HA, Liu Y, Gamazon ER, Alwaseem H, Hite RK, Birsoy K (2023 Jun 6). Integrative genetic analysis identifies FLVCR1 as a plasma-membrane choline transporter in mammals. Cell metabolism, 35(6), 1057-1071.e12. . PMID: 37100056.


9.) Kenny TC, Khan A, Son Y, Yue L, Heissel S, Sharma A, Pasolli HA, Liu Y, Gamazon ER, Alwaseem H, Hite RK, Birsoy K (2023 Apr 25). Integrative genetic analysis identifies FLVCR1 as a plasma membrane choline transporter in mammals Cell metabolism, 35(6), 1057-1071.e12. . PMCID: 10367582.


10.) Sanghai ZA, Piwowarczyk R, Broeck AV, Klinge S (2023 Apr 10). A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation Nature Structural & Molecular Biology, 30(5), 594-599. . PMCID: 10191850.


11.) Harper NJ, Burnside C, Klinge S (2023 Feb). Principles of mitoribosomal small subunit assembly in eukaryotes. Nature, 614(7946), 175-181. . PMID: 36482135.


12.) Berman AY, Wieczorek M, Aher A, Olinares PD, Chait BT, Kapoor TM (2023 Jan 25). A nucleotide binding–independent role for γ-tubulin in microtubule capping and cell division The Journal of Cell Biology, 222(3), e202204102. . PMCID: 9930161.


13.) Hsu DJ, Gao J, Yamaguchi N, Pinzaru A, Wu Q, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie SF (2023 Jan 6). Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells Science Advances, 9(1), eade9120. . PMCID: 9821863.


14.) Choi CH, Barr W, Zaman S, Model C, Park A, Koenen M, Lin Z, Szwed SK, Marchildon F, Crane A, Carroll TS, Molina H, Cohen P (2022 Nov 8). LRG1 is an adipokine that promotes insulin sensitivity and suppresses inflammation eLife, 11(), e81559. . PMCID: 9674348.


Description:

The Proteomics Resource Center (PRC) at The Rockefeller University offers analysis of biomolecules and peptide synthesis for The Rockefeller University community on a subsidized, cost-recovery basis. The Center is also available to other not-for-profit institutions. The Center is located in the south eastern part of The Rockefeller University campus in The Rockefeller Research Building: RRB157. The Center is guided by and reports to a Scientific Advisory Committee (SAC) on a regularly basis. The PRC team members are analytical chemists with expertise in proteomics, metabolomics and peptide chemistry. The corner stone of the Center is liquid chromatography (LC) and mass spectrometry (MS) which we apply to proteomics, metabolomics, lipid and small molecule analysis – see examples of projects analyzed by the Center. The Center is equipped with nano-flow as well as higher flow LC. The majority of our instruments are of the Orbitrap type which offer high mass accuracy and high resolution. A triple quadrupole mass spectrometer is also available. The Center is equipped with, and has expertise in using, a wide array of software for data analysis. A full list of hardware and software are available here. Selected instruments housed in the Center are available for walk-up use. The goal of the Proteomics Resource Center is to extend the limits of sensitivity and broaden the range of tools provided to investigators by implementing and developing novel and useful analytical techniques. To achieve the above we operate in a boutique style, encouraging the PRC scientists and users to collaborate to create a tailored approach to fit the many unique questions that can be answered using our tools and expertise. On a yearly basis, the Center is working with approximately 200 individual users and handles 500+ sample requests making the Center the to-go-to place to discuss proteomic concepts, experiments and data analysis