Nonredundant mass spectrometry: A strategy to integrate mass spectrometry acquisition and analysis

Scherl, Alexander; François, Patrice; Converset, Véronique; Bento, Manuela; Burgess, Jennifer A.; Sanchez, Jean‐Charles; Hochstrasser, Denis F.; Schrenzel, Jacques; Corthals, Garry L.

doi:10.1002/pmic.200300673

Cited by 34 publications

(24 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Over the past years, shotgun proteomics emerged as a key method in the field (30 -32) and various strategies were employed to tackle complex samples including using different MS instruments (33)(34)(35), new fragmentation techniques (36), inclusion lists (37), or repeated sample injections (38). However, none of these methods was as efficient as the approach based on peptide mass exclusion lists (39).…”

Section: Discussionmentioning

confidence: 99%

Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis

Lavigne

Becker

Liu

et al. 2012

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and labelfree large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-

show abstract

Section: Discussionmentioning

confidence: 99%

Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis

Lavigne

Becker

Liu

et al. 2012

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

show abstract

“…To illustrate IE analysis accessing species of lower spectral abundance each entry was highlighted in the round in which it was identified with two or more peptides. In an effort to increase the total coverage, MS-based exclusion has been described in previously LC-MALDI experiments using a single repeat analysis (32,33). With LC-ESI-MS platforms, more extensive exclusion experiments have recently been reported, but these studies are based only on Based on combined analysis of replicates (H1 and H9 hESCs) utilizing all prefractionation approaches, all factors were identified with Ͼ2 unique peptides and were observed in both biological replicates.…”

Section: Discussionmentioning

confidence: 99%

An Enhanced Mass Spectrometry Approach Reveals Human Embryonic Stem Cell Growth Factors in Culture

Bendall

Hughes

Campbell

et al. 2009

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

The derivation and long-term maintenance of human embryonic stem cells (hESCs) has been established in culture formats that are both dependent and independent of support (feeder) cells. However, the factors responsible for preserving the viability of hESCs in a nascent state remain unknown. We describe a mass spectrometrybased method for probing the secretome of the hESC culture microenvironment to identify potential regulating protein factors that are in low abundance. Individual samples were analyzed several times, using successive mass (m/z) and retention time-directed exclusion, without sampling the same peptide ion twice. This iterative exclusion -mass spectrometry (IE-MS) approach more than doubled protein and peptide metrics in comparison to a simple repeat analysis method on the same instrument, even after extensive sample pre-fractionation. Human embryonic stem cells (hESCs)1 are non-transformed cell lines that can proliferate indefinitely in culture, although maintaining the potential to form all primary human cell types (pluripotency) (1, 2). These cells, which originate from the inner cell mass of pre-implantation blastocysts, represent a unique source of human cells for cell replacement therapies and for creating model human systems for understanding disease and development (3). Like other mammalian ESCs, hESCs were originally derived and propagated on replication-deficient mouse embryonic fibroblast (MEF) feeder cells in serum (2, 4), with varying efficiencies (5). At the heart of this variability is a lack of understanding of the regulatory pathways and growth factors that govern hESC self-renewal and pluripotency (6). This ambiguity restricts the application of hESCs in both research and therapeutic applications.We hypothesize that under optimal hESC culture conditions, there exist autocrine and paracrine growth factors, produced both by the feeder cells and the hESCs themselves, that establish the complex microenvironment required to retain hESC potential in culture. Previous genomic-based studies suggested the presence of such networks of hESC transcriptional regulation (7); however, these networks were not correlated to the extracellular microenvironment that ultimately controls hESC fate. Moreover, prior attempts to identify proteins within the hESC microenvironment using MSbased approaches produced few potential candidate regulators and provided little new insight or tangible improvements upon hESC line derivation and culture (6, 8 -11).From the ‡Don Rix Protein Identification Facility,

show abstract

“…To limit the number of spectra and ensure an enriched set of unique spectra, poor-quality spectra could be removed and duplicates identified and eliminated 39,60,61 . Spectra should be searched with at least two algorithms to take advantage of the different selectivities of algorithms (for example, SEQUEST and Mascot).…”

Section: Box 3 Strategy For Large Scale Data Analysismentioning

confidence: 99%

Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book

2004

View full text Add to dashboard Cite

Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a spectrum and sequence: descriptive, interpretative, stochastic and probability-based matching. We review the basic concepts used by most search algorithms, the computational modeling of peptide identification and current challenges and limitations of this approach for protein identification.An unintended consequence of whole-genome sequencing has been the birth of large-scale proteomics. What drives proteomics is the ability to use mass spectrometry data of peptides as an 'address' or 'zip code' to locate proteins in sequence databases. Two mass spectrometry methods are used to identify proteins by database search methods. The first method uses a molecular weight fingerprint measured from a protein digested with a site-specific protease [1][2][3][4][5] . A second method uses tandem mass spectra derived from individual peptides of a digested protein 6,7 (Fig. 1). Because each tandem mass spectrum represents an independent and verifiable piece of data, this approach to database searching has the ability to identify proteins in mixtures, enabling a rapid and comprehensive approach for the analysis of protein complexes and other complicated mixtures of proteins 6,[8][9][10][11][12] . New biology has been discovered based on fast and accurate protein identification [13][14][15][16][17][18] . As tandem mass spectral protein identification has proliferated, it has become increasingly important to understand the rationale of individual database search algorithms, their relative strengths and weaknesses, and the mathematics used to match sequence to spectrum.In this review we discuss the prevailing fragmentation models, spectral preprocessing, methods to match tandem mass spectra to sequences and several approaches to matching tandem mass spectra of peptides whose exact sequences may not be present in the database. Space limitations restrict a detailed description of all algorithms in this rapidly expanding field. Also, some algorithms are proprietary, and thus, details on how they work are unknown. This review should supplement and update earlier reviews on database search algorithms [19][20][21][22][23][24] . Peptide fragmentation and data preprocessingIn tandem mass spectrometry (MS/MS), gas phase peptide ions undergo collision-induced dissociation (CID) with molecules of an inert gas such as helium or argon 25 . Other methods of dissociation have been developed, such as electron capture dissociation (ECD), surface induced dissociation (SID) and electron transfer dissociation (ETD), but gas-phase CID is the most widely used in commercial tandem mass spectrometers. The dissociation pathways are strongly dependent on the collision energy, but the vast majority of instruments use low-energy CID (<100 eV) 26 ....

show abstract

Nonredundant mass spectrometry: A strategy to integrate mass spectrometry acquisition and analysis

Cited by 34 publications

References 19 publications

Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis

Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis

An Enhanced Mass Spectrometry Approach Reveals Human Embryonic Stem Cell Growth Factors in Culture

Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book

Contact Info

Product

Resources

About