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ZipTip^® Pipette Tips

Concentrating and purifying samples for MALDI-ToF MS More

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Sample Preparation for Mass Spectrometry

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Overview

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Ordering Information

ZipTip^® Pipette TipsClear Sorting & Filtering Show Filter

ZTC18S008

ZipTip with 0.6 µL C₁₈ resin

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ZTC18S096

ZipTip with 0.6 µL C₁₈ resin

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ZTC18S960

ZipTip with 0.6 µL C₁₈ resin

960

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ZTC04S008

ZipTip with 0.6 µL C₄ resin

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ZTC04S096

ZipTip with 0.6 µL C₄ resin

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ZTC04S960

ZipTip with 0.6 µL C₄ resin

960

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ZTC18M008

ZipTip with 0.2 µL C₁₈ resin

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ZTC18M096

ZipTip with 0.2 µL C₁₈ resin

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ZTC18M960

ZipTip with 0.2 µL C₁₈ resin

960

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ZTSCXS008

ZipTip with 0.6 µL strong cation resin

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ZTSCXS096

ZipTip with 0.6 µL strong cation resin

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Documentation

References

Reference overview	Application	Pub Med ID
A CROSS-SPECIES STUDY OF PI3K PROTEIN-PROTEIN INTERACTIONS REVEALS THE DIRECT INTERACTION OF P85 AND SHP2 Susanne B. Breitkopf, Xuemei Yang, Michael J. Begley, Meghana Kulkarni, Yu-Hsin Chiu, Alexa B. Turke, Jessica Lauriol, Min Yuan, Jie Qi, Jeffrey A. Engelman, Pengyu Hong, Maria I. Kontaridis, Lewis C. Cantley, Norbert Perrimon, John M. Asara Sci Rep. 2016 Show Abstract Using a series of immunoprecipitation (IP)-tandem mass spectrometry (LC-MS/MS) experiments and reciprocal BLAST, we conducted a fly-human cross-species comparison of the phosphoinositide-3-kinase (PI3K) interactome in a drosophila S2R+ cell line and several NSCLC and human multiple myeloma cell lines to identify conserved interacting proteins to PI3K, a critical signaling regulator of the AKT pathway. Using H929 human cancer cells and drosophila S2R+ cells, our data revealed an unexpected direct binding of Corkscrew, the drosophila ortholog of the non-receptor protein tyrosine phosphatase type II (SHP2) to the Pi3k21B (p60) regulatory subunit of PI3K (p50/p85 human ortholog) but no association with Pi3k92e, the human ortholog of the p110 catalytic subunit. The p85-SHP2 association was validated in human cell lines, and formed a ternary regulatory complex with GRB2-associated-binding protein 2 (GAB2). Validation experiments with knockdown of GAB2 and Far-Western blots proved the direct interaction of SHP2 with p85, independent of adaptor proteins and transfected FLAG-p85 provided evidence that SHP2 binding on p85 occurred on the SH2 domains. A disruption of the SHP2-p85 complex took place after insulin/IGF1 stimulation or imatinib treatment, suggesting that the direct SHP2-p85 interaction was both independent of AKT activation and positively regulates the ERK signaling pathway.		26839216
FOOD PEPTIDOMICS OF IN VITRO GASTROINTESTINAL DIGESTIONS OF PARTIALLY PURIFIED BOVINE HEMOGLOBIN: LOW-RESOLUTION VERSUS HIGH-RESOLUTION LC-MS/MS ANALYSES Juliette Caron, Gabrielle Chataigne, Jean-Pascal Gimeno, Nathalie Duhal, Jean-Francois Goossens, Pascal Dhulster, Benoit Cudennec, Rozenn Ravallec, Christophe Flahaut Electrophoresis 2016 Show Abstract Consumers and governments have become aware how the daily diet may affect the human health. All proteins from both plant and animal origins are potential sources of a wide range of bioactive peptides and the large majority of those display health-promoting effects. In the meat production food chain, the slaughterhouse blood is an inevitable co-product and, today, the blood proteins remain underexploited despite their bioactive potentiality. Through a comparative food peptidomics approach we illustrate the impact of resolving power, accuracy, sensitivity, and acquisition speed of low-resolution (LR)- and high-resolution (HR)-LC-ESI-MS/MS on the obtained peptide mappings and discuss the limitations of MS-based peptidomics. From in vitro gastrointestinal digestions of partially purified bovine hemoglobin, we have established the peptide maps of each hemoglobin chain. LR technique (normal bore C18 LC-LR-ESI-MS/MS) allows us to identify without ambiguity 75 unique peptides while the HR approach (nano bore C18 LC-HR-ESI-MS/MS) unambiguously identify more than 950 unique peptides (post-translational modifications included). Herein, the food peptidomics approach using the most performant separation methods and mass spectrometers with high-resolution capabilities appears as a promising source of information to assess the health potentiality of proteins.		26990205
ISOLATION AND IDENTIFICATION OF MEMBRANE VESICLE-ASSOCIATED PROTEINS IN GRAM-POSITIVE BACTERIA AND MYCOBACTERIA Rafael Prados-Rosales, Lisa Brown, Arturo Casadevall, Sandra Montalvo-Quiros, Jose L. Luque-Garcia MethodsX. 2014 Show Abstract Many intracellular bacterial pathogens naturally release membrane vesicles (MVs) under a variety of growth environments. For pathogenic bacteria there are strong evidences that released MVs are a delivery mechanism for the release of immunologically active molecules that contribute to virulence. Identification of membrane vesicle-associated proteins that can act as immunological modulators is crucial for opening up new horizons for understanding the pathogenesis of certain bacteria and for developing novel vaccines. In this protocol, we provide all the details for isolating MVs secreted by either mycobacteria or Gram-positive bacteria and for the subsequent identification of the protein content of the MVs by mass spectrometry. The protocol is adapted from Gram-negative bacteria and involves four main steps: (1) isolation of MVs from the culture media; (2) purification of MVs by density gradient ultrucentrifugation; (3) acetone precipitation of the MVs protein content and in-solution trypsin digestion and (4) mass spectrometry analysis of the generated peptides and protein identification. Our modifications are:<br />• Growing Mycobacteria in a chemically defined media to reduce the number of unrelated bacterial components in the supernatant.<br />• The use of an ultrafiltration system, which allows concentrating larger volumes.<br />• In solution digestion of proteins followed by peptides purification by ziptip.		26150943
Comparative evaluation of peptide desalting methods for salivary proteome analysis. Nico Jehmlich, Claas Golatowski, Annette Murr, Gesell Salazar, Vishnu Mukund Dhople, Elke Hammer, Uwe Volker Clin Chim Acta 2014		24751662
Using theoretical protein isotopic distributions to parse small-mass-difference post-translational modifications via mass spectrometry. Timothy W. Rhoads, Jared R. Williams, Nathan I. Lopez, Jeffrey T. Morre, C. Samuel Bradford, Joseph S. Beckman J Am Soc Mass Spectrom 2013		23247967
DETERMINIG IN VIVO PHOSPHORYLATION SITES USING MASS SPECTROMETRY Susanne B. Breitkopf, John M. Asara Curr Protoc Mol Biol 2012 Show Abstract Phosphorylation is the most studied protein post-translational modification (PTM) in biological systems, since it controls cell growth, proliferation, survival, and other processes. High-resolution/high mass accuracy mass spectrometers are used to identify protein phosphorylation sites due to their speed, sensitivity, selectivity, and throughput. The protocols described here focus on two common strategies: (1) identifying phosphorylation sites from individual proteins and small protein complexes, and (2) identifying global phosphorylation sites from whole-cell and tissue extracts. For the first, endogenous or epitope-tagged proteins are typically immunopurified from cell lysates, purified via gel electrophoresis or precipitation, and enzymatically digested into peptides. Samples can be optionally enriched for phosphopeptides using immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO(2)) and then analyzed by microcapillary liquid chromatography/tandem mass spectrometry (LC-MS/MS). Global phosphorylation site analyses that capture pSer/pThr/pTyr sites from biological sources sites are more resource and time consuming and involve digesting the whole-cell lysate, followed by peptide fractionation by strong cation-exchange chromatography, phosphopeptide enrichment by IMAC or TiO(2), and LC-MS/MS. Alternatively, the protein lysate can be fractionated by SDS-PAGE, followed by digestion, phosphopeptide enrichment, and LC-MS/MS. One can also immunoprecipitate only phosphotyrosine peptides using a pTyr antibody followed by LC-MS/MS.		22470061
Rapid metabolite identification with sub parts-per-million mass accuracy from biological matrices by direct infusion nanoelectrospray ionization after clean-up on a ZipTip and LTQ/Orbitrap mass spectrometry. John C. L. Erve, William DeMaio, Rasmy E. Talaat Rapid Commun Mass Spectrom 2008 Show Abstract Metabolite identification studies remain an integral part of pre-clinical and clinical drug development programs. Analysis of biological matrices, such as plasma, urine, feces and bile, pose challenges due to the large amounts of endogenous components that can mask a drug and its metabolites. Although direct infusion nanoelectrospray using capillaries has been used routinely for proteomic studies, metabolite identification has traditionally employed liquid chromatographic (LC) separation prior to analysis. A method is described here for rapid metabolite profiling in biological fluids that involves initial sample clean-up using pipette tips packed with reversed-phase material (i.e. ZipTips) to remove matrix components followed by direct infusion nanoelectrospray on an LTQ/Orbitrap mass spectrometer using a protonated polydimethylcyclosiloxane cluster ion for internal calibration. We re-examined samples collected from a prazosin metabolism study in the rat. Results are presented that demonstrate that sub parts-per-million accuracies can be achieved on molecular ions, facilitating identification of metabolites, and on product ions, facilitating structural assignments. The data also show that the high-resolution measurements (R = 100,000 at m/z 400) enable metabolites of interest to be resolved from endogenous components. The extended analysis times available with nanospray enables signal averaging for 1 min or more that is valuable when metabolites are present in low concentrations as encountered here in plasma and brain. Using this approach, the metabolic fate of a drug can be quickly obtained. A limitation of this approach is that metabolites that are structural isomers cannot be distinguished, although such information can be collected by LC/MS during follow-on experiments		18763271
GEL-FREE SAMPLE PREPARATION FOR THE NANOSCALE LC-MS/MS ANALYSIS AND IDENTIFICATION OF LOW-NANOGRAM PROTEIN SAMPLES Marco Gaspari, Vittorio Abbonante, Giovanni Cuda J Sep Sci. 2007 Show Abstract Protein identification at the low nanogram level could in principle be obtained by most nanoscale LC-MS/MS systems. Nevertheless, the complex sample preparation procedures generally required in biological applications, and the consequent high risk of sample losses, very often hamper practical achievement of such low levels. In fact, the minimal amount of protein required for the identification from a gel band or spot, in general, largely exceeds the theoretical limit of identification reachable by nanoscale LC-MS/MS systems. A method for the identification of low levels of purified proteins, allowing limits of identification down to 1 ng when using standard bore, 75 microm id nanoscale LC-MS/MS systems is here reported. The method comprises an offline two-step sample cleanup, subsequent to protein digestion, which is designed to minimize sample losses, allows high flexibility in the choice of digestion conditions and delivers a highly purified peptide mixture even from "real world" digestion conditions, thus allowing the subsequent nanoscale LC-MS/MS analysis to be performed in automated, unattended operation for long series. The method can be applied to the characterization of low levels of affinity purified protei		17763504
COMPARISON OF SDS- AND METHANOL-ASSISTED PROTEIN SOLUBILIZATION AND DIGESTION METHODS FOR ESCHERICHIA COLI MEMBRANE PROTEOME ANALYSIS BY 2-D LC-MS/MS Nan Zhang, Rui Chen, Nelson Young, David Wishart, Philip Winter, Joel H. Weiner, Liang Li Proteomics 2007		17309111
Analysis of modified apolipoprotein B-100 structures formed in oxidized low-density lipoprotein using LC-MS/MS. Takashi Obama, Rina Kato, Yutaka Masuda, Katsuhiko Takahashi, Toshihiro Aiuchi, Hiroyuki Itabe Proteomics 2007 Show Abstract Oxidatively modified low-density lipoprotein (oxLDL) is one of the major factors involved in the development of atherosclerosis. Because of the insolubility of apolipoprotein B-100 (apoB-100) and the heterogeneous nature of oxidative modification, modified structures of apoB-100 in oxLDL are poorly understood. We applied an on-Membrane sample preparation procedure for LC-MS/MS analysis of apoB-100 proteins in native and modified low-density lipoprotein (LDL) samples to eliminate lipid components in the LDLs followed by collection of tryptic digests of apoB-100. Compared with a commonly used in-gel digestion protocol, the sample preparation procedure using PVDF membrane greatly increased the recovery of tryptic peptides and resulted in improved sequence coverage in the final analysis, which lead to the identification of modified amino acid residues in copper-induced oxLDL. A histidine residue modified by 4-hydroxynonenal, a major lipid peroxidation product, as well as oxidized histidine and tryptophan residues were detected. LC-MS/MS in combination with the on-Membrane sample preparation procedure is a useful method to analyze highly hydrophobic proteins such as apoB-100.		17549798

FAQ

Question

Answer

What protocols are available for ZipTip Pipette Tips?

Applications work to-date has focused on sample preparation prior to MALDI-TOF mass spectrometry and direct injection electrospray/nanospray mass spectrometry.

Protocols are available for the following:

Sample Preparation of Peptides or Proteins Prior to MALDI-TOF MS Using ZipTipC18, ZipTipµ-C18 and ZipTipC4 Pipette Tips (TN224) Sample Preparation of Peptides or Proteins Prior to Electrospray / Nanospray MS Using ZipTipC18, ZipTipµ-C18 and ZipTipC4 Pipette Tips (TN072)
Fractionation of Complex Peptide or Protein Mixtures Prior to MALDI-TOF MS Using ZipTipC18, ZipTipµ-C18 and ZipTipC4 Pipette Tips (TN226)
Sample Preparation of Oligonucleotides Prior to MALDI-TOF MS Using ZipTipC18, ZipTipµ-C18 Pipette Tips (TN225)
Enrichment of Phosphopeptides Before MALDI-TOF and Nanoelectrospray MS using ZipTipMC Pipette Tips (TN228)
Purification of Radiolabled Oligonucleotides using ZipTipC18 Pipette Tips (TN230) Peptide Sample
Preparation Prior to MALDI-TOF and Electrospray MS using ZipTipSCX Pipette Tips (TN233)

What is the binding capacity of ZipTipC18, ZipTipµ-C18 and ZipTipC4?

ZipTip Capacity: (when used with saturating amounts of analyte)
ZipTipC18	greater than or equal to 1 µg. Typically 5.0 µg
ZipTipµ-C18	Typically 3.3 µg
ZipTipC4	greater than or equal to 0.5 µg. Typically 3.3 µg
	>
C18 is offered in two bed volumes:
ZipTipC18	a standard bed of 0.6 µL for sample elution in 1 to 4 µL
ZipTipµ-C18	a micro bed of 0.2 µL for sample elution in < 1 µL.

What are the sample elution volumes from ZipTip?

Elution volumes for standard bed volume ZipTip pipette tips are typically 1-4µl.
ZipTipµ-C18 tips have an elution volume of < 1 µl.

When would I need to use a chaotropic agent to enhance binding of my sample to ZipTipC₄?

A chaotropic agent, such as Guanidine HCL (1-4M) which enhances adsorption, should be included in the sample anytime peptide or protein solubility is an issue.

Which single channel and multichannel pipettes are compatible with ZipTip?

ZipTip is compatible with most single channel pipettes that accommodate 10 ml pipette tips. The Biohit Proline® multi-channel pipette from is recommended for 8 channel sample processing.

Proline is a registered trademark of Biohit Oy.

What are the specifications of the C₄ in ZipTipC₄ pipette tips?

C4 -spherical silica, 15 µm, 300Å pore size

What is the ZipTip pipette tip material of construction?

The actual pipette tip is constructed of polypropylene

What types of resins are available in ZipTip pipette tips?

ZipTip pipette tips are currently available with the following resins: C₁₈, C₄, and SCX.

What are the specifications of the C₁₈in ZipTipC₁₈ and ZipTipµ-C₁₈ pipette tips?

C₁₈ spherical silica, 15 µm, 200Å pore size
C₁₈ is offered in two bed volumes:
ZipTipC₁₈ -- a standard bed of 0.6 µl for sample elution in 1 to 4 µl.
ZipTipµ-C₁₈ -- a micro bed of 0.2 µl for sample elution in < 1 µl.

Which ZipTip is best for processing my sample?

ZipTipC₁₈ for desalting oligonucleotides and low molecular weight proteins and peptides (up to 50,000 Da). Final sample elution in 1-4 µl
ZipTipm-C₁₈ for desalting oligonucleotides and low molecular weight proteins and peptides ( up to 50,000 Da). Final Sample elution in <1 ml
ZipTipC₄ for desalting low to intermediate molecular weight proteins (3,000 - 100,000 Da). Final sample elution in 1-4 µl.

Resin	Compatible Analytes
C₁₈ Resin (0.6 µL or 0.2 µL bed volumes)	Oligonucleotides or small (<50 kDa) proteins/peptides in aqueous solution
C₄ Resin	Proteins or peptides (3 kDa – 100 kDa) in aqueous solution
Strong cationic resin (SCX)	Peptides in solution with organic solvents or detergents

Materials
Pipette Tip	Polypropylene
C₁₈ and µ-C₁₈ Resin	Silica, 15 µm, 200 Å pore size
C₄ Resin	Silica, 15 µm, 300 Å pore size
SCX Resin	Strong cation exchange, 12 µm, 300 Å pore size
Volumes, µL
Pipette tip	10 µL
Resin Bed	0.2 or 0.6
Capacity
ZipTip_C18	Typically 5 µg when used with saturating amounts of analyte
ZipTip_µ-C18	Typically 2.0 µg when used with saturating amounts of analyte
ZipTip_C4	Typically 3.3 µg when used with saturating amounts of analyte
Dimensions
Tip Length	31 mm
Tip ID (top)	3.375 mm
Tip OD (top)	5.8 mm
Temperature, °C	4至70 °C
pH Range	pH1.5 – pH13.5; pH2 – pH12 for 24 hour exposure

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Concentrating and purifying samples for MALDI-ToF MS More

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