title: A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization.
abstract: Targeted mass spectrometry assays for protein quantitation monitor peptide surrogates, which are easily multiplexed to target many peptides in a single assay. However, these assays have generally not taken advantage of sample multiplexing, which allows up to ten analyses to occur in parallel. We present a two-dimensional multiplexing workflow that utilizes synthetic peptides for each protein to prompt the simultaneous quantification of >100 peptides from up to ten mixed sample conditions. We demonstrate that targeted analysis of unfractionated lysates (2 hr) accurately reproduces the quantification of fractionated lysates (72 hr analysis) while obviating the need for peptide detection prior to quantification. We targeted 131 peptides corresponding to 69 proteins across all 60 National Cancer Institute cell lines in biological triplicate, analyzing 180 samples in only 48 hr (the equivalent of 16 min/sample). These data further elucidated a correlation between the expression of key proteins and their cellular response to drug treatment.
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Brian K
authors.initials: BK
authors.lastname: Erickson
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Rose
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Craig R
authors.initials: CR
authors.lastname: Braun
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Alison R
authors.initials: AR
authors.lastname: Erickson
authors.affiliation: Cell Signaling Technologies, Danvers, MA 01923, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Knott
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Graeme C
authors.initials: GC
authors.lastname: McAlister
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Wühr
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Joao A
authors.initials: JA
authors.lastname: Paulo
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: Robert_Everley@hms.harvard.edu.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Everley
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: Steven_Gygi@hms.harvard.edu.
authors.forename: Steven P
authors.initials: SP
authors.lastname: Gygi
mesh_terms: D000903:Antibiotics, Antineoplastic / Q000494:pharmacology; D015415:Biomarkers / Q000378:metabolism; D045744:Cell Line, Tumor; D004317:Doxorubicin / Q000494:pharmacology; D057166:High-Throughput Screening Assays; D006801:Humans; D013058:Mass Spectrometry; D009363:Neoplasm Proteins / Q000378:metabolism*; D009369:Neoplasms / Q000188:drug therapy / Q000378:metabolism* / Q000473:pathology; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D013997:Time Factors; D014157:Transcription Factors / Q000378:metabolism; D057188:Workflow; D000092468:Bromodomain Containing Proteins
chemical_list: D000903:Antibiotics, Antineoplastic; D015415:Biomarkers; D004317:Doxorubicin; D009363:Neoplasm Proteins; D020543:Proteome; D014157:Transcription Factors; C116750:BAZ1B protein, human; D000092468:Bromodomain Containing Proteins
keywords: NCI-60; cancer; high-throughput; isobaric tag; multiplexing; proteomics; targeted proteomics