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Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

ABSTRACT: There is an unmet technical challenge for mass spectrometry (MS)-based proteomic analysis of single mammalian cells. Quantitative proteomic analysis of single cells has been previously achieved by antibody-based immunoassays but is limited by the availability of high-quality antibodies. Herein we report a facile targeted MS-based proteomics method, termed cPRISM-SRM (carrier-assisted high-pressure, high-resolution separations with intelligent selection and multiplexing coupled to selected reaction monitoring), for reliable analysis of low numbers of mammalian cells. The method capitalizes on using "carrier protein" to assist processing of low numbers of cells with minimal loss, high-resolution PRISM separation for target peptide enrichment, and sensitive SRM for protein quantification. We have demonstrated that cPRISM-SRM has sufficient sensitivity to quantify proteins expressed at ?200,000 copies per cell at the single-cell level and??3000 copies per cell in 100 mammalian cells. We envision that with further improvement cPRISM-SRM has the potential to move toward targeted MS-based single-cell proteomics.

SUBMITTER: Shi T

PROVIDER: S-EPMC6123794 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

Shi Tujin T Gaffrey Matthew J MJ Fillmore Thomas L TL Nicora Carrie D CD Yi Lian L Zhang Pengfei P Shukla Anil K AK Wiley H Steven HS Rodland Karin D KD Liu Tao T Smith Richard D RD Qian Wei-Jun WJ

Communications biology 20180806

There is an unmet technical challenge for mass spectrometry (MS)-based proteomic analysis of single mammalian cells. Quantitative proteomic analysis of single cells has been previously achieved by antibody-based immunoassays but is limited by the availability of high-quality antibodies. Herein we report a facile targeted MS-based proteomics method, termed cPRISM-SRM (carrier-assisted high-pressure, high-resolution separations with intelligent selection and multiplexing coupled to selected reacti ...[more]

PMID: 30271983

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Project description:Untargeted analysis of a composite house dust sample has been performed as part of a collaborative effort to evaluate the progress in the field of suspect and nontarget screening and build an extensive database of organic indoor environment contaminants. Twenty-one participants reported results that were curated by the organizers of the collaborative trial. In total, nearly 2350 compounds were identified (18%) or tentatively identified (25% at confidence level 2 and 58% at confidence level 3), making the collaborative trial a success. However, a relatively small share (37%) of all compounds were reported by more than one participant, which shows that there is plenty of room for improvement in the field of suspect and nontarget screening. An even a smaller share (5%) of the total number of compounds were detected using both liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS). Thus, the two MS techniques are highly complementary. Most of the compounds were detected using LC with electrospray ionization (ESI) MS and comprehensive 2D GC (GC×GC) with atmospheric pressure chemical ionization (APCI) and electron ionization (EI), respectively. Collectively, the three techniques accounted for more than 75% of the reported compounds. Glycols, pharmaceuticals, pesticides, and various biogenic compounds dominated among the compounds reported by LC-MS participants, while hydrocarbons, hydrocarbon derivatives, and chlorinated paraffins and chlorinated biphenyls were primarily reported by GC-MS participants. Plastics additives, flavor and fragrances, and personal care products were reported by both LC-MS and GC-MS participants. It was concluded that the use of multiple analytical techniques was required for a comprehensive characterization of house dust contaminants. Further, several recommendations are given for improved suspect and nontarget screening of house dust and other indoor environment samples, including the use of open-source data processing tools. One of the tools allowed provisional identification of almost 500 compounds that had not been reported by participants.

Project description:ObjectiveTo determine the specific type of amyloid from nerve biopsies using laser microdissection (LMD) and mass spectrometric (MS)-based proteomic analysis.Design, setting, and patientsTwenty-one nerve biopsy specimens (17 sural, 3 sciatic, and 1 root amyloidoma) infiltrated by amyloid were studied. Immunohistochemical subtyping was unable to determine the specific amyloid type for these 21 cases, but the clinical diagnosis was made based on additional testing. Clinical diagnosis was made through evaluation of serum monoclonal proteins, biopsy of bone marrow for acquired monoclonal immunoglobulin light chain amyloidosis, and kindred evaluations with DNA sequencing of transthyretin (TTR) and gelsolin (GSN) genes. Our study included 8 cases of acquired monoclonal immunoglobulin light chain amyloidosis, 11 cases of transthyretin amyloidosis (3 with the Val30Met mutation, 2 with the Val32Ala mutation, 2 with the Thr60Ala mutation, 1 with the Ala109Ser mutation, 1 with the Phe64Leu mutation, 1 with the Ala97Ser mutation, and 1 not sequenced), and 2 cases of gelsolin amyloidosis (1 with the Asp187Asn mutation and 1 not sequenced). One patient with transthyretin amyloidosis and 1 patient with gelsolin amyloidosis with no specific mutation identified were diagnosed based on genetic confirmation in their first-degree relative. Congophilic proteins in the tissues of these 21 cases underwent LMD, were digested into tryptic peptides, and were analyzed using liquid chromatography electrospray tandem MS. Identified proteins were reviewed using bioinformatics tools with interpreters blinded to clinical information.Main outcome measureSpecific amyloid type was ascertained by LMD tandem MS and compared with clinical diagnosis.ResultsSpecific types of amyloid were accurately detected by LMD/MS in all cases (8 cases of acquired monoclonal immunoglobulin light chain amyloidosis, 2 cases of gelsolin amyloidosis, and 11 cases of transthyretin amyloidosis). Incidental serum monoclonal proteins did not interfere with detection of transthyretin amyloidosis in 2 patients. Additionally, specific TTR mutations were identified in 10 cases by LMD/MS. Serum amyloid P-component and apolipoprotein E proteins were commonly found among all cases.ConclusionsProteomic analysis of nerve tissue using LMD/MS distinguishes specific types of amyloid independent of clinical information. This new proteomic approach will enhance both diagnostic and research efforts in amyloidosis and other neurologic diseases.

Dataset Information

Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

Publications

Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

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