2021
DOI: 10.1101/2021.04.24.441211
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Exploring functional protein covariation across single cells using nPOP

Abstract: Many biological functions, such as the cell division cycle, are intrinsically single-cell processes regulated in part by protein synthesis and degradation. Investigating such processes has motivated the development of single-cell mass spectrometry (MS) proteomics. To further advance single-cell MS proteomics, we developed a method for automated nano-ProteOmic sample Preparation (nPOP). nPOP uses piezo acoustic dispensing to isolate individual cells in 300 picoliter volumes and performs all subsequent preparati… Show more

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Cited by 36 publications
(50 citation statements)
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“…With a better understanding of today's limits, such as the maximum loading channels that should be used in amplificationbased experiments, further advances will continue to chip away at these limits [59]. One key limitation is the sample preparation, and two preprints that were posted in early 2021 have demonstrated nanoliter semi-automated workflows to address these limitations [26,60]. These are reaping obvious dividends, resulting in some of the most comprehensive singlecell proteomes described to date (Figure 6).…”
Section: Discussionmentioning
confidence: 99%
“…With a better understanding of today's limits, such as the maximum loading channels that should be used in amplificationbased experiments, further advances will continue to chip away at these limits [59]. One key limitation is the sample preparation, and two preprints that were posted in early 2021 have demonstrated nanoliter semi-automated workflows to address these limitations [26,60]. These are reaping obvious dividends, resulting in some of the most comprehensive singlecell proteomes described to date (Figure 6).…”
Section: Discussionmentioning
confidence: 99%
“…These methods aim to achieve similar objectives, such as efficient delivery of peptides from single cells to the MS instruments via miniaturized sample preparation ( 1 ), but differ in the approaches used for achieving these objectives. For example, sample preparation volumes can be reduced by using microfabricated wells ( 30 ) or by using droplets on the surface of a slide ( 31 ). All single-cell MS methods can be classified either as label free or as multiplexed, and these categories have associated advantages and disadvantages as previously reviewed ( 1 , 2 ).…”
Section: Trade-offs Between Single-cell Proteomics Methodsmentioning
confidence: 99%
“…Sample preparation throughput increased with the introduction of automated multiwell-plate methods, such as minimal ProteOmic sample Preparation (mPOP) ( 21 , 39 , 40 ) and automated preparation in one pot for trace samples (autoPOTS) ( 41 ). A further increase is afforded by a droplet sample preparation method (nano-ProteOmic sample Preparation [nPOP]) that enables the simultaneous and automated preparation of over 2000 single cells in droplets on a slide surface ( 31 ). In addition to increasing throughput, the simultaneous processing of thousands of cells reduces the batch effects associated with different sample preparation batches.…”
Section: Highly Parallel Sample Preparationmentioning
confidence: 99%
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“…The isobaric reporter ion fragments corresponding to labels applied to single cells, if within the intrascan linear dynamic range of the instrument, can be used for both peptide identification and quantification. [21][22][23][24] Although other single cell technologies such as single cell RNAseq have been sorting and analyzing single cells for over a decade with increasingly sophisticated technology, relatively little of this can be applied to proteomics approaches. 25,26 While new technologies such as nanoPOTs 27 , nPOP 23 and ProteoChip 24 are improving these aspects, technical challenges in sample preparation may be the biggest limiter to entry into single cell proteomics.…”
Section: Introductionmentioning
confidence: 99%